I have filed an internal bug report for the CCSM3.0 "C" compset exact restart problem. Unfortunately, because of very imited resources, I am unsure as to when, or even if, this problem will be corrected in the released version of the code.
Something I should have pointed out to you right at the outset of this post is that the "C" compset, as configured "out of the box" in CCSM3.0, is not suitable for scientific experimentation. The CCSM documentation alludes to this, in the Introduction of the CCSM3.0 User's Guide, section 1.5, albeit somewhat indirectly:
"Although CCSM3.0 can be run ``out of the box'' for a variety or resolutions and component sets, it must be stressed that not all combinations of component sets, resolution and machines have been tested or have undergone full climate validations. "
The documentation goes on to list three variations of the "B" compset that have been scientifically validated; what is left unsaid is that the "C" compset is, as configured, useful mainly for testing purposes.