When the ?> tag is in a comment block, it gets parsed as part of the script, not the comment.  If the <?php is on the same line, it doesn't have any effect and still gives a problem.  Sample code for problem:

// If the new config file has the beginning 
// <?php but not the closing ?> due to an 
// onforseen file problem, delete the bad file
// before it is included in the next run and 
// causes problems

However, if the above comment section were enclosed between /* .... */, it works fine.  It just seems to be with the // comment style