Claudia, we tied the issue down to employees who initially have negative checks created. The client has a few employees who have garnishments. They set up the default garnishment amount in the deduction definition which always causes a negative check. After the payroll calculation, they go back in and adjust the amount of the deduction based upon the employee's net check amount before the deduction. The negative check forces the direct deposit flag off regardless of the setting in employee maintenance. The client now knows to ensure they reset the flag when the deduction amount is adjusted and the paycheck is recalculated
I hope that helps. (We created a quick and dirty crystal report lists the checks from a payroll run for employees who have the direct deposit flag set to try in employee setup and have the direct deposit flag turned off in payroll entry. The client now includes running the report as part of their regular process to check for similar situations before the arise.
Hope this helps.