on a 4.0 sp1 W1 version we have the payment tolerance activated.
ACY have 5 decimal places on unit amount rounding precision and on amount rounding precision.
when a payment tolerance take place when applying LCY payment to ACY invoice (s) only 2 decimals are considered, and vendor ledger entries remain open with ex: 0.003 as remaining amount.
i changed the rounding parameters for the LCY the same way, but still having these remainings.
application rouding precision is set to 5 decimals too.
Navision is using amount rounding precision for payment tolerance of G/L Setup or Currency amount rounding precision.
I don’t use often payment tolerance. Have you checked if this problem persists in other versions such as 4.0 SP3.