Even though it sounds like you have fixed the problem. In the future your script would probably be more efficient if you listed all the files of one extension like you did, but instead of listing the others to a file, take the entries from the first file, chop off the last 3 chars, append the 3 from the other extension, and then check to see if that file exists or not by using GetFileAttr. If it returns a non-zero value, the file exists so delete both files.
This method would reduce the number of embedded loops and file operations.

Luck