Sorry, finally found it.
You're talking about SH4?
Removing or un-installing a game will not cause it to lose code, as you put it.
Did you post this over at the SH4 forums?
You would get a lot more answers over there.
Also you may want to check out this:
http://www.subsim.com/radioroom/showthread.php?t=107783
Tech help thread.
Also this handy guide to SH4:
CLICK ME
When uninstalling did you delete your SH4 Folder in My Documents? Before installing again?
Let me know how you get on
