If Jane is cashing each of the checks separately and putting it into individual envelopes, there's strong evidence that she's a messenger, and the check payees are the beneficiaries of these transactions. That means you have one CTR with one Section B entry (Jane) and multiple Section A entries (one for each payee). This, of course, presents horrific logistic problems, since you probably don't have ID info on any of the payees.
If Jane presents the checks as one transaction, and you give her cash for the total, with no breakdown per payee, then I think Jane or the company is the beneficiary, and Jane is still the transactor.
As for any thought of exempting the issuer of the checks under the payroll exemption, don't even think about it. That's only available to employers who pay their employees in cash (no check issued).
For some pretty obvious reasons, this sort of transaction is a royal pain. If the employer insists on having Jane act as messenger on payday, you should insist that the employer gather and provide the address and ID information on all the payees. Maybe you even get the employer to fill in all the Section A and B items on the CTR so it's ready when Jane comes to the bank.
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John S. Burnett
BankersOnline.com
Fighting for Compliance since 1976
Bankers' Threads User #8