Since both transactions were, by definition, conducted on Mom's behalf and total over $10,000, you have to file. Because the deposits are made to joint accounts, you have to include Section A entries for the joint owners.
For paper CTR filers:
File one CTR, with Mom in the first Section A, multiple transactions and multiple persons checked in item #1. Check "conducted on own behalf" in Section B. Add section A entries for Son and for Father. List the combined cash total in item 26, and provide both account numbers.
Since Son conducted one of the deposits, you could swap him to the first Section A and include Mom and Dad in Section A's on the reverse.
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John S. Burnett
BankersOnline.com
Fighting for Compliance since 1976
Bankers' Threads User #8