Posting the website or file where the javascript link is located will greatly help. It might not be your computer but the actual script that is at fault. If the computer is locking up for at least a minute then I can guarantee that it is the script because a reformat is definately going to clear up all your computer's problems.
PS. To check your version of IE, hit Help > About.
PS 2. No virus can survive a reformat.
PS 3. FAT32 is simply a hard disk file system type and has no role in this working or not, but knowing that you use FAT32 I can recommend you switch to NTFS as FAT32 isn't the latest and greatest file system anymore. HOWEVER, If you ever use DOS bootdisks or other OSes on your laptop (like Windows 95/98 or Linux) you won't be able to access your hard disk from those OSes. You okay with that? Cool, open a command prompt (Start > Run > type CMD > Press enter, type convert, press enter, if you get told that 'conversion will take place at next reboot' or similar then reboot, leave the computer alone for awhile (a good idea would be to do this overnight) and then you'll have integrated encryption/compression available.
PS 4. As a precaution I recommend antivirus software - AVG Free and ZoneAlarm together are a good combination.