Amiga 1200 issues!!

[Oldsmobile_Mike]

When you say "get written over", are you saying they're being replaced by older versions of those files, or just becoming corrupted? Are you running any installer scripts (to install games, for example) that could be writing over those files?

You don't say if you're operating off a hard drive but I assume so. Your issue could also be caused by a failing hard drive. It happens. You can replace it with a CF card like this:

http://amigakit.leamancomputing.com/catalog/product_info.php?products_id=883

You should still check the caps on your motherboard but that's not what's causing your current problem.

[Oldsmobile_Mike]

it seems to occur after installing software.

Troubleshooting 101, retrace your steps. If the files get corrupted when you install software, it's probably the install process.  Can you break it down, exactly what you're doing to install software?

Also, are you using FFS, or some other exotic disk format like PFS or SFS?

[Oldsmobile_Mike]

How large are your partitions?