Annotation randomly gone missing when using Print Organizer

I am using AECOsim BD 08.11.09.747 in conjunction with 08.11.09.829 in an attempt to find a solution to fix a mysterious issue (some annotation tags gone missing randomly) while using Print Organizer to batch print 500 - 1000 PDF sheets.  This problem does not occur if I print one sheet at a time using the standard print command in ABD, which is not ideal before a deadline.  I have tested any possible causes that I can come up with and applied to the existing DV, Design, Drawing and Sheet models to no avail.  My conclusion for the time being is that my project files are not causing the problem, instead the print organizer may be unable to process the complex annotation being generated through the use of rules and Reference Presentation settings.  The unfortunate part of this is the generated PDFs through Print Organizer yield to different results each time as if some cached files are interfering with the generation of these final PDFs.  I have cleaned up all local temporary files including the re-built of my local preference files.  One of the telling signs is that when I open a sheet file, the screen halts for about 5-10 seconds right after the plans are loaded.  After this pause the annotation tags are not displayed when all tools are loaded.  However, if I mouse over the area where the annotation tag is supposed to be then it actually highlights it.  If I mouse click this "ghost like" object then the annotation mysteriously appears.  If I open the reference manager and click the file, then all missing annotation tags suddenly appear!  I made sure my video driver is up-to-date, I have tried this with a Win7 64 bit PC and Win 8.1 64-bit PC with the same results.  This behavior I believe may be caused by the Print Organizer's inability to load and print the sheet files properly.  I can't provide a sample as this happens in a unpredictable manner.  I have generated four different sets of PDFs (8 sheets each), and the results are not the same.  I have checked all the settings within the print organizer thoroughly, but have not been able to fix this issue.  The mystery perhaps lies in-between the complexity of the DV files being referenced as nested objects in the Sheet Model, which the Print Organizer is unable to process because I can always generate a perfect PDF sheet using the AECOsim BD's built-in print command, not ideal before a deadline.  Any help is greatly appreciated as I have pretty much exhausted all possibilities that would resolve this mystery.  Thanks in advance.  Ken Shigemtisu - Shalom Baranes Associates, PC