I think the issue is back to what Twey said originally:
1. When you are copying it the CHMOD permissions are disabling it's execution (make it '777').
2. Perhaps the actual data is not being transferred properly-- so be sure the text always shows up properly in the file once copied, and perhaps check things like character encoding if that for some odd reason might cause a problem.
The other test here is to copy a file that is not included, then run that independently. If that runs, but the included version does not, then the inclusion is the issue, not the copying. Of course if it does copy and then doesn't run it's the copying that is a problem.
I hope this points you in the right direction. Sounds like a strange problem.
Also, having used the copy function a couple times, I found it useful to look at the comments and code suggestions below it on the php.net page, and there are a few things (like copying a directory recursively) that are helpful and might help with your problem, such as showing you how to copy with correct permissions (assuming that's an issue, someone else must have run into it before).
