Sounds like an issue support will need to look into. Can you try with v6.2 which is our latest build as well?
what do you mean by "via Packages"? Do you install AC not via ePO but by hand / software distribution etc? Are there any other security products on the server - e.g. AV/VSE, encryption, ...?
So if I get you right, than reboot works as long as AC is not enabled (observe mode)?
- try the latest version 6.2.x -> if the problem is gone, than some compatibility issue
- try to install via ePO - if that works - than some problem with your manual install
- does it make any difference if you switch do update mode instead of observe mode?
- you could also try the following ePO > policy catalog > Solidcore 6.2.0: Application Control > Application Control Options (Windows) > (<your policy>) => set Self-Approval AND Advanced Options
btw: we did a rollout to 100+ W2003 without that issue...