Track Pad On Sony VAIO Not Working

I recently installed a new HDD (Seagate ST9500424AS; p/n 9RW143-567) in my Sony VAIO VPCEH11FX and installed the OS using the Sony VAIO Recovery Media Kit (VPCE_10FX Series 989203008). During the installation, I selected the default or normal settings. A short while (1-2 weeks) after the installation was complete, I noticed that the track pad was not working after enabling it using Fn+F1. (The pointing device dialog box DOES appear when I press Fn+F1 and shows that it will toggle between enable & disable). I took the computer into Fry's (where I bought it) and they booted a different OS (I think it was Windows XP) using a CD. Using this OS, the track pad worked. So it was confirmed it wasn't a hardware issue. I proceeded to contact Sony. They had me do the following:

1) download the latest drivers & driver updates and install both. This didn't fix the problem.
2) uninstall 'Alps Pointing-device for VAIO' and run the .exe files for the driver & update. This didn't fix the problem.
3) boot the computer to recovery mode (press F10 when it starts); I noticed that the track pad was working in this mode.
4) Confirm that the other ALT keys functioned properly. (they do function properly)

The Sony rep asked me to confirm the type of HDD I installed (I forget what specifically he was interested in), but upon my reading him the part number, he confirmed the HDD was compatible.The Sony rep then suggested I either recover the system to a previous version/date and see if the track pad is working. (he seems to think some software I installed might have prevented the track pad from working) He also suggested I could reformat the HDD and reinstall the entire OS. I've balked at doing either, as I'm guessing there is an issue with the registry.