I had the exact same porblem but my ftp program was the culprit. The default setting was making a log file in each folder as I uploaded the files the only place it caused a problem was in the captcha related folders. Once I went thru all the folders and deleted the log files the problem went away.
here is my
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By the way I don't know about PHP files But when I used Frontpage years ago it played havoc on cgi files such as changing permissions. So I always excluded any type of script files from frontpage and just used a ftp program. I believe the newer version allows you to exclude certain folders now.