[OS X TeX] pdf loses information

[Alex Hamann]

I am aware that the following problem is poorly described and requires some debugging. I nevertheless decided to go ahead and ask the list - maybe someone can point out how to best approach this issue.

I recently had to do a lot of beamer presentations. I usually create them in TeXShop (instead of my generally preferred Aquamacs). I noticed that on my system (SL 10.6.2, TeX Live 2009, TeXShop 2.29) sometimes the pdf file becomes corrupted and loses information. This results in partly white slides, loss of several slides or the whole presentation in the pdf file (tex file is fine thought). The pattern appears to be the following: I work on the tex file, run XeLaTeX several times on the file and get correct pdf-output.  I then shut my whole system down and return the next day to continue my work. On opening the tex file with TeXShop the pdf is then (often) shown with the problems mentioned above.  One XeLaTeX run brings all the slides back but it is really the pdf that is corrupt since opening that file with skim (or any other viewer for that matter) shows the white slides.
I can not yet see a pattern (e.g. if only a specific type of slides is affected, say, those containing lists) and can also not directly connect this behavior to the shutting down/restart process. 
Is anybody else seeing this too? Otherwise I will start testing with other editors, command line, etc.

Alex