You can't be sent to prison for not having a TV licence, but you can for not paying a fine.
However tens of thousands of people don't pay fines (or fail to pay them on time) every year but there will only be a tiny handful of them who are actually sent to prison. (Those will generally only be people who openly defy the courts).
So you've almost certainly got nothing to worry about. Indeed it sounds as if it might just be an administrative error which has resulted in the the court service failing to have noticed that you'd actually been paying the fine in accordance with the arrangement agreed to by the Court. Or perhaps your bank has made an error? Or was the standing order (or direct debit) due for processing when you'd temporarily not got enough in your account for the bank to honour the demand for payment?
Get hold of a copy of your bank statement. (If you've not had a 'proper' statement recently, your bank branch should be able to print off a document showing your transactions in the past few months. If you get hold of such a document, ask the cashier to put the bank's official stamp on it, and to sign across it).
If you can prove to the Court that you've made the payments, you've got nothing to worry about at all. Similarly, if you can show that the deficit in your payments has come about through a genuine mistake, there wil again be nothing to worry about.
The Court won't consider imprisonment unless you stick two fingers up at the Magistrates and tell them exactly where they can stick their fine!
Chris