Considering the solution - I have been thinking for several days that perhaps this issue stemmed from a problem with the disk on the original system. It might be slightly damaged - somehow not enough to prevent it from booting, but enough to cause the seen issues in the clonezilla image.
If I cared, I could run chkdsk /r on the system a few times, then take a clonezilla image again, and then try restoring that.
meh.
