So how does this work.
one lady deposits $6,000 or so each for two seperate entities during the same day.
one of the entities is a phase 2 exempt entity.

No CTR because she only deposited $6k on the non-exempt entity??

That is correct; if you have filed an exemption for one of the entities then there is not CTR to file in either case (one exempted, the other not greater than 10,000).

Wait a minute...don't we have one person walking in to the bank on a single business day and conducting more than $10,000 - it just so happens to be on behalf of two different beneficiaries? Why wouldn't this be reportable?

Actually, when I was in Georgia the FDIC told us this would have been reportable for that very reason.

I was under the impression that you ignore the exempt transaction in situations like this. No CTR.

I believe that when a business account is exempted, qualified exempt transactions in that account are ignored for CTR purposes, as if they never occurred (to quote a leading guru).

Therefore, it doesn't matter that there was a transaction to another account at the same time, unless that specifc transaction met the CTR limits and was not also exempt.

That's correct. If I walk into your bank with $50,000 cash and deposit $45,000 of it to the transaction account of an exempt business and $5,000 to my personal account, you only have to concern yourself with the $5,000 deposit for CTR purposes, and therefore would not file one.