While setting up my new iPad yesterday, I experienced a strange problem. iTunes (on Windows) would repeatedly crash with a problem in msvcrt10.dll when trying to copy the apps to the iPad.
In the Apple support forums, I found the explanation and a workaround for this problem: It seems like iTunes 11.4 introduces a but (that is still present in iTunes 12) that causes a crash when apps are stored on network share and referenced using a UNC path. In my case, the Music folder (which is the default location for the iTunes library) is redirected to a UNC path pointing to a DFS share. Interestingly, this bug only affects apps, not music or videos.
In order to make the apps sync again, the path that iTunes uses for referencing the files needs to be shared to a regular path with a drive letter. This can either be achieved by copying the apps to a local driver or mapping the network share to a drive letter. Either way, all apps need to be deleted from the iTunes library (but not deleted on disk) and re-added using the regular path. Obviosuly, iTunes has to be configured to not automatically copy files to its default library location. After this change, the synchronization should work. Finally, the apps can be deleted again and re-added using the UNC path - once the apps are on the device (with the newest version) iTunes will not try to copy them again, thus avoiding the bug.
However, I find it annoying that this bug has been known since mid of September and still has not been fixed by Apple.