I had this machine that had an issue with the anti-virus blocking the "Software Deployment" schedule.
I fix the anti-virus (create one exception to c:/kworking) and then used the 'Deploy Now' option to update all software.
After about 2 hours, I went there and check the 'Status-->By Machine' and it shows double lines for almost each software (see the image)
I run AUDIT (not sure if that helps, but I did) and still the same.
Any ideas what that could be?
Have had this issue several times. Contact support and they will provide you with a script to run on the database, or they will help you clean up the database.
Could be nice to see a permanent fix ....