I also have this problem.  URLs of the form

/section.php?id=90&filename=746_March%20News%20From%20The%20Network.pdf

are being saved as HTML files rather than pdf files.

The server is returning the correct content-type value but it does not seem to
be being checked by httrack.

I've also tried removing the entry for php in the MIME settings so this
section is completely blank, but this did not make a difference.

I am using the latest version (3.40-2 (+swf)) which I just downloaded.

Other than this, httrack is great - I've used plenty of mirroring/site
archiving programs and this is the best by far.