Firstly we need to check which release of Monarch 8 you have. There were a coule of releases after the PDF functionality was introduced that enhanced the capability and addressed most of the problemsthat can exist with pdf files. There are so many pdf writing programs around and so many parameters to deal with that not all of them come up perfectly constructed pdf's even when they look OK.
Ideally you will have installed up to the Monarch 8.02 update. If not I would recommend downloading the update from the Datawatch support site and installing it and then try the pdf file again.
Secondly there are some controls within the interpretation program to try to provide users with the ability to adjust the interpretation of the pdf beyond the automatic interpretation that Monarch applies when the file is opened.
Have you experimented with the variable setting to see if anything improves? If so what was the result?
To some extent the adjustments can really only be understood after experimentation but the internal Monarch Help references may also provide some ideas about which way to adjust things.
Lastly, for now, there are some files which are simply a mess internally and people have had some success in opening such files in a PDF editing capable application (Adobe Acrobat is the most obvious example!) and re-saving them. That seems to result in a new version which is more amenable to Monarch Processing. There are several related posts in the forum about this approach.
Do any of these suggestions help you?