I'm having the very same problem.  I've had the problem for so long that I've narrowed it down to movement WITHIN the Batch Enter Screen. Any time I have to go back and correct a typo or change an amount on a transaction, the very next NEW transaction will not recall the account. SO frustrating. I then have to save the transactions at that point, go to preferences, RE-CHECK the box, and go back to Batch Enter Transactions.

I noticed this stream goes back quite some time...it really needs to be fixed.