CGI not working, as if not in ascii

This is not consistent so I don't know for sure where the problem is.

I'm uploading files from a domain to a new ISP.

In one of the domain directories I had no problem with cgi , I just had to set permissions and it was ok.

In one of the other domain directories I could not figure out why the scripts would not run.
I tried uploading from another FTP program that requires a selection for ascii or binary for each upload.
I selected ASCII and uploaded the files and they worked.

I tried then uploading the same file with smartftp, and it didn't work again.
I uploaded the same file with the other program and it did work again.

I'm new to using smartFTP, so am I missing something, or do you have any other ideas.