They asked for clarification as to whether the 50% rule set in stone, no matter what had been done with those accounts. It's not surprising that they did so, since his attorneys were stressing that point.
My guess is that they saw the transfer of half-ownership as a fig-leaf, enabling Manafort to get around the IRS requirements on a technicality. (It might not have been so obvious if his wife hadn't been the other party 
) The judge's response was that functional control of the accounts meant that he needed to report them. (I think the shelf company question may have been related to the FBAR question as well.)
Asking about reasonable doubt can go both ways. I think it's possible that they were asking for assurance that they did not need to satisfy themselves on every wild-ass but-what-if they could conjure up.
No questions directly about the tax charges or bank fraud, though. We'll know soon enough.
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