JRE install caused loss of most .exe files!!

WinXP home, sp2
After downloading and installing JRE, windows cannot find most of my C: drive (program) .exe files...INCLUDING GHOST!.....even after removing JRE.
Somehow IExplorer worked after a few tries. Cannot manually find them either.
ran CHKDSKR, no luck.
Checked for W32/Pate worm/virus, not there.
All programs not in my C: drive work.
PLEASE ADVISE

I reinstalled Ghost 9.0 and restored my C: partition....First time I needed to rely on a backup ..TG.
Which brings my system back to Win. service pack 1a.
Why would JRE corrupt my C: partition??
I'd like to find out before I try installing JRE once more.
PLEASE ADVISE
=RR=
BTW...I believe I need it to run OpenOffice.org and some Adobe products.

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