Hi Helen
Before panicking, do the following -
Make sure everything is retrieved into the Ledger and posted.
Run an Open Payables report as of fiscal year-end and see if it ties to the Payables balance as of period 12.
If it does, then you have a timing difference which will wash out over time. If it doesn't, then something went wrong, and as Doug says, it can be any number of things.
Here's an example - if you scan through the Payables account activity and see transactions that have a source code other than AP (such as GL), then that is going to be your problem. Nobody should be making GL journal entries to that account, without knowing exactly what they are doing.
Steve