I know that there was an issue noted on Aug 5 that talked about when Reconciling the HSA account, but I experience this on a more regular basis (last 3-4 months).
I receive a paycheck that is entered with the Paycheck Wizard into my main Checking Account.
There are amounts that are put into other accounts: HSA, 401K, savings account and an another checking Account.
When Reconciling one of the other accounts, the main checking amount is changed to a payment to the other account.
For example: Paycheck is $2000, HSA=$250, 401K=$300, Savings=$100, 2nd Checking=$125 and the balance is left as a deposit for $1225. (values are for discussion).
When the Paycheck is validated (I open and check it) and then the Main Checking is reconciled, all is well. Deposit of $1225 is noted.
Move to one of the other accounts, and see that correct amount is listed as deposit, Reconcile the other account. All is well in that account, e.g. 2nd Checking account for $125 is a deposit.
Return to the Main Checking, and the paycheck entry now is not a deposit, but rather a payment of the amount for the recently reconciled account, e.g. checking account now shows as a payment of $125 rather than the deposit. Open the Entry, and it has all the correct values, exit with saving, and the deposit returns.
Now before someone says it is a display issue, when the reconcile of the "other account" occurs, the balance in now incorrect in the main checking, and shows in the account window as well as when you enter the account until you open and save the paycheck again.
I also note it is not always consistent, and not always only the last paycheck, today, I was trying to reconcile the HSA account, and I noticed in the account window that the main checking amount was off by about 2 paychecks…. and sure enough, I found that the last two paychecks had been changed to payments of $250. Open and save, all is restored.
Now that I know what is occurring it is easy enough to go fix, but it is very annoying to have to fix.