There are a lot of different PDF writing programs around and some can produce code that is not always easy to read with pdf reading applications. It sounds like the source for some of your reports may suffer from that.
If you have access to a copu of Acrobat (not the reader version but the full version, preferably the Pro level) you could try opening the file for edit and re-saving it. There are a number of posts in the forum suggesting that doing so often provided a solution for a problem file.
It might also be interesting to see what sort of output you get if you use the Export to Text (or similar name) function in the reader application. If this is badly formed it might also suggest some internal problems with the pdf instructions.
Some time ago (pre 8.01) there was a thread asking for problem file examples (files to be provided) for investigation. It is possible that your problem files might also be of interest since this sort of development is always likely to be a candidate for constant adjustments.
Addressing the "Timeout" first:
Monarch does "Timeout" at 10 seconds.
I have come across this a few times. When Monarch opens a file it writes to your Temp Directory. If there isn't enough Free Space, a "Timeout" error will be thrown. So it may be time to do a little housekeeping.
I have also seen this error occur when the PDF file contains errors due to the way it was produced. Monarch tries to make sense of it and open it, but due to eratic formatting, it can't.
Since you state that when a file does open for you the structure of the data is not aligned, if it is grossly misaligned, the later could be true.
I would be more than happy to send you a Non-Disclosure Form, if it would be helpful in getting the file to me. We work with sensitive material often and I have no problem destroying files after working to resolve an issue.
Feel free to contact me:
Datawatch Tech Support