OK, it definitely sounds like Java while it may have reinstalled, didn't configure it self correctly. Which is not unusual for some software installers.
So lets try the easy fix, before we go with the more complicated manual registry changes.
If you go in the the control panel look for the icon for JAVA, double click it.
(START > SETTINGS > CONTROL PANEL)
On the General tab, in the "Temporary Internet Files" section click on the "Settings" button.
In the new window that pops up -
Click Delete Files in the "Disk Space" section.
In the next window uncheck the box for Trace and Log files, leaving the Applications and Applets checked.
Click OK.
Click Apply.
(Doing this will delete the special JAVA temp files and force any previously downloaded javascript files and applets to re downloaded. )
Next go to the Advanced tab.
Find the object in the list called "Default Java for Internet Browsers" click the plus to expand it.
If both check boxes for IE and Mozilla are checked, then un-check them and click apply then ok (little popup window saying you will need to restart the browser)
If none of them or one of them is checked then check uncheck the one that is checked and click Apply, then ok.
The idea is to cycle them through till they are all checked again, this will cause the software to reset the registry entries. Hopefully correcting the problem.
Once all done click on and reboot the PC (It is Windows after all)
Let us know the results. If that fails then its the manual registry entry phase, and that's not fun.
HTH,
