Run Acrobat, uncheck the web integration box and ok your way out.
Sorry, this bug has been around for over 5 years and I've yet to find a fix.
I'm running Win98SE with IE 6.02 and Acrobat Reader 6.03. (Actually, the same thing happens now on my roomate's PC after he installed XP SP2)
PDF links open a new window with a small icon in the upper left corner.
Works fine if I can download the file and double click(some just try to open automatically).
Also works OK in Firefox...
Adobe implies that it might be a missing ActiveX control/plug-in, but doesn't list the files anywhere for version 6. (Just for ver 7 which doesn't run on Win98SE)
I have done a 'Repair' and tried de-selecting 'Open in Browser' in the Reader's options.
Searched all over for a fix.... Anyone have any ideas?