I have the same issue.

I have tried what you have explained. Unmatched then Matched. Shows on the match to be matched with Bank deposit # 7011, but in reconcile it still is a separate deposit. Have done the unmatch 4 times with the payment received deposit then bank deposit, Tried with bank deposit first to match to Payment recieved deposit with same result of separate lines in reconcile.  with the same result.

It has happened 2 times in August, 2 times in January, 2 times in February, 2 times in March, 1 time in May.

with other deposits that went as suppose to be, in those months, totally strange,