Since some deposits aren't showing up when you begin reconciling a particular account, I'd initially recommend confirming your transactions are dated within the date range you're trying to reconcile for.
If they are, you'll want to check if they've already been reconciled.
Here's how:
In your left navigation bar, go to Accounting, then Chart of accounts.
Find the account you're working with.
Click its View register option.
If a transaction's already been reconciled, it will display an "R" in its Checkmark (✔) icon column.
In the event you've identified that your deposits in question have already been reconciled, but shouldn't have been, there's two ways you can go about correcting them. One option is to manually change the transaction's status, the other method is to have a ProAdvisor user undo your prior reconciliation(s).