JBIG2 files open only after 'rebuilding'....

I use a third party app to generate PDF files using JBIG2 compression. I notice unusual behavior in Adobe Acrobat 8 Standard that does not occur in 9 or 10 (Std or Pro).
When v8 opens these files, it performs a "Rebuilding" process before the file is opened and displayed. This, in turn, causes the file to be altered and subjects the user to selecting if they want to save the changes before closing the file. These files are generated as image-only. If these same files are created without the JBIG2 compression, this prompt is not displayed and no save before close prompt is displayed. This leads me to believe that Adobe 8 performs some type of conversion in order to "understand" the file.
Can someone help me understand what this "rebuilding" is doing and why it only happens in v8?

We have a network of nearly 40 macs, Panther Server, mostly panther clients but the newer machines are on 10.4.
All of the newer machines exhibit the problem that iSchwartz is mentioning. this happens locally with files on the desktop and also for files saved to the server. I contacted Apple regarding this but because we only have APP on our desktop machines not the server they said it must be a server issue and I would have to pay for an incedent. NICE. They said that there is no issue like this with 10.4 or 10.4 interacting with a 10.3 server (I beg to differ).
I have tried various things to correct this e.g. repairing permissions, complete reformat and clean install on a test machine, turning off IPv6 on both the server and the client (though as I said before this issue occurs on the client desktop as well, so it is not "a server issue")
Interestingly I would agree that this is some kind of refresh issue as if you navigate to the directory using the terminal and listing the contents all the files are there both locally and on a server volume.
Additionally Files that cannot be seen by the client which saved them can be seen by other clients. These two points would fairly clearly point at a refresh issue. (by the way disconnecting and reconnecting to a shared volume is not a fix, opening/closing a folder or changing the view does not force a refresh)
Any help would be much apreciated, one machine I would accept as a glitch but all of the 10.4 machines in the building looks more like an issue to me.

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