What sort of environment are you running under (NT, Novell server, peer-peer) and what operating system do you have (NT, Win 98, etc)? I highly doubt user error is the cause.
Which specific fields are affected (invoice total, extended invoice total after tax, any others)?

Are you able to duplicate this error (ie when you come across an inaccurate invoice, can you make the invoice total double by following certain steps)? Also, is there any sort of pattern for this (ie happens for same customer, each invoice has a particular item, a specific entry # in the batch, etc)?

Make sure you have the current 990215 release of version 65A installed if it isn't already.