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If I do understand your question all right (sorry, am not a native English speaker), I do believe you are mixing up two things. If you want indeed to publish to PDF (and not to SWF or EXE), you'll get a multimedia PDF (in which a SWF can play) but in that case the user really do need the Adobe Reader 9, previous versions do not support multimedia PDF.
What seems a bit contradictory is that you start with mentioning an issue with a PDF that should be called from a CP-slide. The problem there could be that you were linking to an absolute path on your PC when browsing, can you check that? If you introduce simply the name of the PDF and you make sure that the PDF and the CP-published files (normally HTML, JS and SWF) are uploaded in the same folder, the CP will find the PDF. I think you now have a 'broken link' because of an absolute path reference for the PDF.
Thank you so much for your help, Lilybiri!
You were absolutely right, I was confusing 2 separate things! First I de-selected the 'Export PDF' option when publishing, as I realized that it was exporting my entire project to PDF. To fix the issue regarding the PDF that wouldn't display, I had to include the link to the location where our LMS pulls the PDF document (and all other files associated with my project) from in the URL field of the click box properties. This finally solved my issue and explained why the published file outside of the LMS was working beautifully (because my PC can locate the document on my drive), but the LMS couldn't find the document.
Ahhh... problem solved. Thanks so much. I can sleep well tonight!!