This affects 1.3 as well, but the fix is intrusive enough it is better to just depend on workarounds.
The issue is that if you add adjustments those are often not picked up on the next update. This shoudl be fixed by storing the max entry_id of acc_trans at last run with the cr_report table and updating it on each update of the report. This way, new records can be pulled in.
At present I think these should come in as new lines which can then be selected together. That could be changed over time, but for now, let's keep it simple.