Did you run an audit after uninstalling MSE?

Run Latest Audit

Yes, I did.

ok run this below VBS file to affected machine manually ..it will show the result current list of AV product installed  you can see if any conflict found ..if you found conflict you need run clean up

' to test on a remote system, set strComp = TheComputerNameOfTheRemoteSystem

' script will fail if you don't have permission to query the system

Dim strComp, iAVCount, iFWCount, iASCount, sAV, sFW, sAS, bXP

Dim objFSO, objFolder, objShell, objTextFile, objFile

Dim strDirectory, strFile, strText

strDirectory = "c:\logs3"

strFile = "\Summer.txt"

strText = "Book Another Holiday"

strComp = "."

Set objWMIService = GetObject("winmgmts:{impersonationLevel=impersonate}!\\" & strComp & "\root\cimv2")

Set colOperatingSystems = objWMIService.ExecQuery ("Select * from Win32_OperatingSystem")

For Each objOperatingSystem in colOperatingSystems

  if instr(objOperatingSystem.Caption, "XP") <> 0 then

     call XPSub

     bXP = True

  else

     call VistaSub

     bXP = False

  end if

Next

select case iAVCount

   case 0

  sAVMsg = "WARNING - No AntiVirus Product Detected!" & vbnewline  & vbnewline

   case 1

  sAVMsg = "AntiVirus Product:  " & sAV & vbnewline  & vbnewline

   case else

  sAVMsg = "WARNING - " & iAVCount & " AntiVirus Products Detected:" & vbnewline & vbtab & sAV & vbnewline  & vbnewline

end select

if bXP = False then

  select case iASCount

      case 0

     sASMsg = "WARNING - No AntiSpyware Product Detected!" & vbnewline  & vbnewline

      case 1

     sASMsg = "AntiSpyware Product:  " & sAS & vbnewline  & vbnewline

      case else

     sASMsg = "WARNING - " & iASCount & " AntiSpyware Products Detected:" & vbnewline & vbtab & sAS & vbnewline  & vbnewline

  end select

end if

select case iFWCount

   case 0

  sFWMsg = "No 3rd Party Firewall Detected." & vbnewline  & vbnewline

   case 1

  sFWMsg = "Firewall Product:  " & sFW & vbnewline  & vbnewline

   case else

  sFWMsg = "WARNING - " & iFWCount & " Firewall Products Detected:" & vbnewline & vbtab & sFW & vbnewline  & vbnewline

end select

Msgbox sAVMsg & sASMsg & sFWMsg, , "Security Product Detection VBS by KITS"

Sub VistaSub

  Set oWMI = GetObject("winmgmts:{impersonationLevel=impersonate}!\\" & strComp & "\root\SecurityCenter2")    

  Set colAVItems = oWMI.ExecQuery("Select * from AntiVirusProduct")

  For Each objAntiVirusProduct In colAVItems

      If LenB(objAntiVirusProduct.DisplayName) > 1 Then

     sAVState = right(hex(objAntiVirusProduct.productstate), 4)

     if left(sAVState, 1) = "1" then

         sAVActive = "Enabled"

     else

         sAVActive = "Disabled"

     end if

     if mid(sAVState, 3, 1) = "0" then

         sAVCurrent = "Up to Date"

     else

         sAVCurrent = "Outdated!"

          end if

          if lenb(sAV) < 1 then

         ' only one here

         sAV = objAntiVirusProduct.DisplayName & " (" & sAVActive & ", " & sAVCurrent & ")"

         iAVCount = 1

     else

         ' multiple products end up here

         sAV = sAV & vbnewline & vbtab & objAntiVirusProduct.DisplayName & " (" & sAVActive & ", " & sAVCurrent & ")"

         iAVCount = iAVCount + 1

     End if

      End if

  Next

  Set colASItems = oWMI.ExecQuery("Select * from AntiSpywareProduct")

  For Each objAntiSpywareProduct In colASItems

      If LenB(objAntiSpywareProduct.DisplayName) > 1 Then

     sASState = right(hex(objAntiSpywareProduct.productstate), 4)

     if left(sASState, 1) = "1" then

         sASActive = "Enabled"

     else

         sASActive = "Disabled"

     end if

     if mid(sASState, 3, 1) = "0" then

         sASCurrent = "Up to Date"

     else

         sASCurrent = "Outdated!"

          end if

          if lenb(sAS) < 1 then

         ' only one here

         sAS = objAntiSpywareProduct.DisplayName & " (" & sASActive & ", " & sASCurrent & ")"

         iASCount = 1

     else

         ' multiple products end up here

         sAS = sAS & vbnewline & vbtab & objAntiSpywareProduct.DisplayName & " (" & sASActive & ", " & sASCurrent & ")"

         iASCount = iASCount + 1

     End if

      End if

  Next

  Set colFWItems = oWMI.ExecQuery("Select * from FirewallProduct")

  For Each objFirewallProduct In colFWItems

      If LenB(objFirewallProduct.DisplayName) > 1 Then

     sFWState = right(hex(objFirewallProduct.productstate), 4)

     if left(sFWState, 1) = "1" then

         sFWActive = "Enabled"

     else

         sFWActive = "Disabled"

     end if

          if lenb(sFW) < 1 then

         ' only one here

         sFW = objFirewallProduct.DisplayName & " (" & sFWActive & ")"

         iFWCount = 1

     else

         ' multiple products end up here

         sFW = sFW & vbnewline & vbtab & objFirewallProduct.DisplayName & " (" & sFWActive & ")"

         iFWCount = iFWCount + 1

     End if

      End if

  Next

end sub

sub XPSub

  Set oWMI = GetObject("winmgmts:{impersonationLevel=impersonate}!\\" & strComp & "\root\SecurityCenter")  

     Set colAVItems = oWMI.ExecQuery("Select * from AntiVirusProduct")

     For Each objAntiVirusProduct In colAVItems

            If LenB(objAntiVirusProduct.DisplayName) > 1 Then

           if objAntiVirusProduct.onAccessScanningEnabled = True then  

               sAVActive = "Enabled"

           else

               sAVActive = "Disabled"

           end if

           if objAntiVirusProduct.productUpToDate = true then

               sAVCurrent = "Up to Date"

           else

               sAVCurrent = "Outdated!"

           end if

           if lenb(sAV) < 1 then

               ' only one antivirus here

               sAV = objAntiVirusProduct.DisplayName & " (" & sAVActive & ", " & sAVCurrent & ")"

               iCount = 1

           else

               ' multiple antivirus ends up here

               sAV = sAV & vbnewline & objAntiVirusProduct.DisplayName & " (" & sAVActive & ", " & sAVCurrent & ")"

               iCount = iCount + 1

           End if

         End if

     Next

  Set colFWItems = oWMI.ExecQuery("Select * from FirewallProduct")

  For Each objFirewallProduct In colFWItems

      If LenB(objFirewallProduct.DisplayName) > 1 Then

     if objFirewallProduct.enabled = True then  

         sFWActive = "Enabled"

     else

         sFWActive = "Disabled"

     end if

          if lenb(sFW) < 1 then

         ' only one here

         sFW = objFirewallProduct.DisplayName & " (" & sFWActive & ")"

         iFWCount = 1

     else

         ' multiple PRODUCTS end up here

         sFW = sFW & vbnewline & vbtab & objFirewallProduct.DisplayName & " (" & sFWActive & ")"

         iFWCount = iFWCount + 1

     End if

      End if

  Next

end sub

Check Microsoft Security Center and see if MSE is still listed.  If it's not then run a new baseline audit (warning you will lose the old baseline).  Make sure you give it about 10 minutes to update the data.  If you're still seeing a conflict then you can either a) enter a support ticket or b) ignore it since it's not there.

Need to run a baseline audit.

Looks like that was it, it needs a new baseline audit and not a latest audit. Thanks

I spoke too fast. It did clear for one test computer, but since, it hasn't cleared for others.

Looks like a baseline and then a latest does the trick.

The baseline should do it (I've also had success with only running a latest).  Typically, you just have to wait long enough for the audit to complete and send the XML files to the KServer for processing.  Regardless, glad it worked.