I've written about this before and it's still happening. Thank you, but I've been using this program for six years or so and I don't need instructions on how to make reconciliation work - it's a bug.
It happens during checkbook account reconciliation and only if I have entered data for after the reconciliation period. Use today's for example: September 27 to October 25, and I have entered all that data, plus a weeks worth after that, to 3 November, for instance. Usually, the account will not reconcile as some of the entries (checks) bleed back into the reconciliation period and leave the account unbalanced, in this case by $594. Yes, the dates were accurate.
I have been able to work around it by marking each entry after the reconciliation period as "Void;" this works, then I balance the account. After balancing I then return to the account and remove the "Void" marks. Repeat every month.
I hope this gives you enough info to fix it - it's annoying. Currently I'm using MacOS 10.12.1, but it was problematic prior to 10.12.