Odd, I have never had any problems with firefox and my program, in fact I use firefox on all my machines.
When you uninstalled firefox it doesnt remove your profile. I did have a problem in firefox once a while back where something was corrupt in my profile casing the problem. So to find out if that is what is happening with yours we just need to rename the firefox profile and have it make a new one.
What version of Windows are you on?
So on my WIndows 7 the profile is located at
C:\Users\(Your Username Here)\AppData\Roaming\Mozilla\Firefox\Profiles
And in the folder is your profile, simply rename it and then open firefox again.
Lets see how that goes
Shane