Makes absolute sense. Some of the companies set the meter at a rate which is designed to recover the cost of units used and any fixed charges for the billing period (that applies to any two rate tariffs or tariffs with primary/secondary rates as well). Therefore lets say on average you use 1000 units per quarter and they have a basic charge of £10 per quarter. If the published rate per unit is 10p then the cost of your bill would be £110. If the meter was set to recover 10p only you'd have a supplementary bill at the end of the quarter of £10. Because of that the meter in this case would be set at say 11p per kWh to make sure you had no outstanding amount at the end of the quarter, or whatever the billing period is.
Factor in any outstanding debt and that gets added onto the unit "price" as well. Some of the companies are also increasing rates at the moment because THEY underrecovered because of the prices rises over the last 12 months or so. i.e. you might have been paying 8p but the actual price increased to something higher than that. Because the suppliers couldn't get round the meters to reset them in time you may have been underpaying and the new rate is designed to cover your current costs and any "debt" which may have accrued.
Not all the companies are doing this though, some are writing it off as it's not your fault you've incurred the debt, not all though.
You need to speak to the supplier and find out exactly what the situation is. Meantime have a look at this lot, it's a while since I've done anything on domestics but they used to be one of the cheapest suppliers for those on prepayment meters.
http://www.ebico.co.uk/en/open/pages/whatwedoen.php