Links in web browser opposed to Adobe Pro

I have a problem that I am trying to fix. I have an intranet map application(opened in IE) that allows in house users to *click* a feature to open a general Information.pdf about that map feature (ie. street sign). the general information pdf has links to additional pdf's about that sign(inspection reports, etc)
The preferences>Internet in Adobe Pro 9.2 are set to open in the program not the web browser because editing capabilities for the users are manditory.
So the problem is that when the general information.pdf is opening it opens in an IE temp directory fashion and not in its network location (\\jacas02\structures\app..... etc). The link to the additional documents are then looking for those additional documents in a location relative to the temp file location(C:\Documents and Settings\.....etc) and not the actually document location on the network. Therefore the document/file can not be found.
If we enable the pdf to be opened in the web browser everything works fine but we don't have the adobe pro functionality. Any suggestions or links to related articles would be greatly appreciated.
Also, can adobe pro functionallity be enabled in the adobe IE web browser?
thanks for any suggestions!
jac

This is a map application served by ArcGIS Server. I don't think that is relevant though. I suspect that this is between IE and Adobe.
How would setting a base URL be applied? All of the General Info pdf's are in one folder on the network \\jacas02\structures\app\INFO
Then within that INFO folder I have additional folders that contain all of the linked documents that are not being found because adobe is opening the file from IE in a temp location.
If I set the base URL to \\jacas02\structures\app\INFO should that work even though it is a 'UNC'?
thanks for you interest, it seems that this should be a easy issue to solve but its got me stumped.
Also, forgot to add. The links have always been relative in adobe as long as you keep them organized the same as when you created the links in adobe.
jac

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