Strange situation indeed.
Do you export to PDF directly from the Data Merge panel, or do create a merged InDesign file fist, and then export to PDF?
Is this replicable? Does it happen with one file or more than one file? What operating system? You'll need to provide us with more information if you're expecting others to help you.
I create the merged indesign file from the data merge panel. I then merge all records to a new indesign file. All items are created in the new indesign file. Master page items no problem. It's when I then export to pdf that I have the problem of missing ojects, text and so forth in the pdf. Usually the problems show up around page 3 and after. For some reason the first two or three pages will show fine. I have learned to be very careful about assuming that the pdf is correct.
I am using a mac mini 10.7.5 with Adobe Creative Premium Suite 5.5, all applications are up to date. Mac OSX is showing up to date as well.
Which export-profile / settings do you use?
Did you try different export-profiles for creating the PDF?
I tried different export settings. Once I was exporting as acrobat 7 (1.7), dropped back to Acrobat 4 (pdf 1.3) and everything was fine. Next time I exported from a merge I set it at Acrobat 4 had the same problem, missing items.
Last week I had the same problem, I moved everything off the master pages and exported Acrobat 7 with no problem. It seems that if the problem shows up it's time to rearrage start again.