The ability to mine data from PDF files was introduced in Monarch v8.00, and Datawatch soon discovered that while the PDF "standard" was anything but standard. It seems that, as you've indicated, there are many, many PDF authoring programs and systems and the output of some play nice with Monarch, and some, well, not so much...
Version 9 was better at interpreting PDF files than was v8, and v10 should be better yet.
In the meantime, I'd recommend that you download and apply the patch for v8 to bring your installation up to [URL="http://22.214.171.124/support/downloads/m802_upd.exe"]v8.02[/URL].
No guarantee that it'll work for the problem you described, but at least you'll know that you'll take care of any known bugs in v8 that were addressed by the patch.