RE: Beginning and ending balances are correct.

The formula is:

Beginning balance + Deposits - Payments = Ending Balance.

So, if the beginning balance matches the bank statement, then if your total payments and total deposits match, then you're done as the ending balance will then match. (Some bank statements include a total for each of these things.)

Find the differences by de-selecting everything and then using the bank statement, select the matching transactions in reconcile one at a time, and mark the paper statement's transaction as matched/selected. You'll eventually find what is missing or different in your books compared to the bank statement. Then fix that and then continue reconciling until everything matches.