Yes, recent upgrade to 2.02.
Yes, I am at a hosting company but this is a dedicated box and they normally will not touch it (I'm responsible for it). I suppose that they could have changed something on the box anyway but it would be very unlike them to do so.
If it helps you to see the behavior:
http colon slash slash aetonline.org slash store slash download.php?article=ecqp2683
The above should resolve to a PDF in a subfolder. Instead, it tries to download download.php
http colon slash slash aetonline.org slash store slash download.php?article=wntyxxx4
The above should download a (large) zip file. It creates a zero or 1-byte zip instead
http colon slash slash aetonline.org slash downloadnow.php
This is a hardcoded MP3 file. Works fine