A couple of things to check out -- what's the effective date or settlement date of the HSA credits? There could be something in the payroll software that makes that date a few days after payday so the employer can "sit" on the funds for a couple of days.
The other thing is the practices of the HSA-holding bank.
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John S. Burnett
BankersOnline.com
Fighting for Compliance since 1976
Bankers' Threads User #8