Distro - Ubuntu 10.04 standard
Problem - Left mouse button fails to work on certain apps such as Firefox web pages although you can close the window with the upper right hand X.
Attempts at resolution - replace mouse with known good mouse, try different users etc.
Results - The problem is happening for only one user (myself). 3 other users have no problem at all.
So it is not hardware related but user related.
I think the problem happened when I mounted an external hard drive to add wallpaper but did not copy the wallpaper over to my home directory. I have auto mounted the drive at boot, but that did not fix the problem.
Being some what of a newbie, I do not know where to look to see were the problem is.
Can someone please point me in the right direction.

If only some applications have this, maybe it is realted to window toolkit, not sure but i think firefox use GTK+

Yes you are correct about Firefox using GTK. Now the next question is what is the best way to troubleshoot this? Remember I am a newbie but I am not afraid of the command line.
Thanks

Almost ALL apps in Ubuntu are GTK+.