You CAN file for less than the FFIEC amount of $25,000 if you suspect suspicious activity. IMO its easier to explain why you're filing than to say, "well we think its suspicious but FFIEC guidance says only file if the amount is $25,000 or more" and not file. But that's just me.
Refer to bullet four on page 60 of the FFIEC manual:
"Transactions conducted or attempted by, at , or through the bank (or an affiliate) and aggregating $5000 or more if the bank or affiliate knows or has reason to suspect that the transaction:
- has no business or apparent lawful purpose or is not the type of transaction that the particular customer would normally be expected to engage in....."