Hi Kobi.
We are in same situation. Format, install Windows, join domain, etc all ok but apps only install some, no all.
We have seen smsts.log and failed to install apps, but others install correctly and appears with new computers and older "randomly". NAA is activated, in DP's is activated "Allow clients to connect anonymously". In our case, applications are downloaded all on "ccmcache".
If someone can help us and Kobi, we are very grateful.
Thanks!!