<<When my computer started back up again all my programs have been disabled and i cant access them.>>
There are a couple of known fixes for this, if this is the major problem right now...with malware not an issue.http://www.dougknox.com/xp/file_assoc.htm
, try the EXE File Association Fix from the group listed.WARNING: This involves a registry edit. Before proceeding with any edit of the registry, it is highly suggested that users back up the registry.
A good tool for doing so (before running the above) is ERUNT Registry Backup Tool - http://www.snapfiles.com/get/erunt.html
<<I did have the fake windows xp virus pop ups which i know arent the real thing but they have now gone>>
Did that occur after you did your attempted malware removal...or before?
Did you scan your system with your updated AV program...after using Malwarebytes?
Reason I ask is that I volunteered to to clean a couple of local systems that had various problems...and I found that Malwarebytes doesn't remove everything (nothing does, that's why several tools are needed to protect a system) and running my AV program afterwards...was a good idea.
Your answers will let us know how we might approach your situation, thanks.