yes I am experiencing this as well..
I entered a deposit into the checking account with a liability account as the other account so as to create a loan to the company. When I checked my bank statement, in FA, it shows a negative balance.
I then voided this transaction, and tried just a journal entry, which was to credit the checking account and the debit side to the liability account. Again when I checked the "bank statement" balance, it shows a negative balance.
It seems kindof counter-intuitive that making a deposit into the checking account should take money out of it.