I'm unable to recreate the symptoms you describe (500 error when clicking Update Currency button) on a fresh clean install of v1.3.9f (there have been no changes to that part of the code since 1.3.9a), and I've tested on various servers, including one of GoDaddy's cheap freebie-hosting servers which usually have a myriad of problems due to being overloaded and serving up banner ads. I did find that their server timed out a few times causing some odd displays and sometimes odd errors, but the currency update didn't trigger any errors.

I'm inclined to think that the problem's not related to the PHP files, unless you've got some that are damaged due to edits or failed FTP transfers.