PHP not working properly after upload

I uploaded a large number of files and now my site isn't working properly.

I have a file being included which contains only variables. Now i get "signature = ""; ?>".

Just found out something decided to replace an $ with an ?> and as it happened after the upload i'm guessing it's the ftp, although i don't know how/ why it would do that. I also had a power outage half way through downloading the upload.

Hello ..

The SmartFTP client does in no case temper the data it transfers. Try to upload the file again.