On all of your machines, or just some of them? Are you assigning all users to all devices? If so, perhaps the SBFS is full or close enough to it that the errors are thrown because something can't happen in there. If you look at your SafeBoot Client Status window, what does it show for SbFs Free Space?
It appears that the issue is caused by the clients Safeboot file system has reached and exceeded it's maximum allowed limit. The resolution is as follows:
To increase the size of the SBFS to the maximum (32mb) do the following:
=> In the "SbAdmin" folder create a file called "defscm.ini". This file holds pre-set parameters used in the SCM.ini file. => This file should contain: [Disk] Sbfs.defaultsize=32 Create a new installation set and deploy it to a client, the file size of the SBFS should now be 32 mb. This procedure cannot literally be found in the "Device Encryption Administrators Guide". But you can put it together by searching the guide for defscm.ini and scm.ini.
From build 5300 the size can be increased up to 512 mb.
think LONG AND HARD about assigning so many users - do you REALLY need so many people to be able to access each PC? I expect not, and your real problem is you don't know who is actually accessing each box.
3000 users, apart from making sync very slow and long, and adding a huge amount of network traffic, is also a huge security risk.
you'd be better off looking at the autodomain scripts to do clever user assignment rather than this approach.