So I'm thinking that maybe it has to do with my having run a Period End at September 30th, as the Adjustment transaction shows in History and not in Current. The Cash transaction the adjustment was applied to is an October cash transaction - I actually made 2 adjustments to this October cash transaction, one dated October to debit the AR and the one in question dated September to credit the AR (I had mistakenly applied a payment on the date that I was entering it instead of the correct September date). When I run the ATB at October 31st it is fine, although it doesn't show the Adjustments but they cancel each other out. The Customer balance is fine, the AR gl account is fine, it was just that the ATB wasn't tying in.

Thanks for all of your help - I think I'll just leave it alone as there's not a data integrity error and everything reconciles and balances now.

Cheers!!