Well, I just got some clarification from NCUA on the shared branch issue.
Basically, the shared branch agreement states which institution is supposed to file the CTR. However, even if the receiving share branch receives the cash, the "home" Credit Union still has to ensure that the CTR was filed and filed correctly. Therefore, the share branch is supposed to FAX or send the CTR to the "home" Credit Union.
If a member deposits cash and different share branches throughout the day, the "home" CU is then responsible to file the CTR (multiple transaction) if the cash threshold is met.
If the share branch files the CTR and there are errors, the home Credit Union is responsible for filing an amended CTR.
If the home Credit Union suspects structuring, it should take appopriate action.
Of course, the issue remains that the data processing systems that support the share branch transaction reporting can be somewhat less than steller in the manner in which information is accessible to the home Credit Union, making it difficult to immediately determine the amount of cash in a mixed deposit. This is an issue that the NCUA is aware of, but so far it is up to the Credit Unions to try and push the issue with their processors.