Now comes the first hard evidence that customers have voted with their feet - with 62,000 leaving the energy firm.
The David vs Goliath battle in which perseverance and patience literally paid off.
The Chancellor has urged energy companies to reconsider their price hikes, in an interview with ITV News.
Problems with billing systems can "turn households budgets upside down" and energy companies owe it to their customers to make any changes as smoothly as possible.
Citizens Advice chief executive Gillian Guy said:
– Gillian Guy
The knock-on effect of poor billing systems can turn household budgets upside down. Many people do not have the spare cash to cover the cost of a large bill that suddenly lands on their doorstep.
While we recognise Npower is receiving more complaints because it is starting to get over some of the earlier issues, it needs to do more to stop consumers' problems escalating.
Offering repayment plans and discussing ways they can help consumers from the off will nip issues in the bud and remove the need to complain.
The number of complaints about npower and Scottish Power doubled in the first quarter of 2014, according to Citizens Advice.
Citizens Advice and Citizens Advice Scotland point to problems with new billing systems as to why there was a sharp rise in complaints.
Complaints about npower rose from 306.8 for every 100,000 customers during the closing months of 2013, to 592.4 between January and March - or one complaint for every 168.8 customers.
Scottish Power complaints increased from 100.5 per 100,000 customers to 197.7 in the first quarter.
All suppliers saw an increase in complaints, although the rise was only slight for some, it added.
Energy firm Npower has apologised again for customer service problems that have taken "longer than planned" to be resolved.
In a statement the company said its CEO Paul Massara had written to customers last year to apologise for the issues, which were "caused by the implementation of a new computer system".
The company says a number of measures have been introduced to tackle the problems:
- An extra 650 have been assigned since December to help resolve problems
- Late invoice and complaints data will be published monthly
- An additional £20 million will be invested this year to deal with customer service issues
- A ban on outbound telesales calls if late billing targets are missed
An investigation into "prolonged customer service failings" at Npower is to be launched, energy regulator Ofgem has announced.
Under the watchdog's new powers to enforce fair treatment of consumers, Npower now faces a financial penalty or redress payment it is found to have broken the rules.
Earlier this month Npower said it would no longer send bills to customers who left it more than six months ago if the company itself was to blame for the delay.
The move followed reports of households switching away from Npower only to receive bills months, and in some cases over a year, later.
One former customer tweeted MoneySavingExpert.com saying they left Npower last June and only recently received a bill for more than £1,000, while another said they had received a £350 bill 16 months after they left.
It is a billing fiasco stretching back a year. You might think not getting a bill would be good news - but late billing has left Npower customers not knowing how much they owe, then getting big and unexpected bills.
I'm told 414,000 accounts have been affected. Now Ofgem are using new powers to threaten a £356 million fine and a ban on outbound telesales calls if the company fails to get this mess sorted out by the end of August.
I spoke to Npower this lunchtime, it says the problems will be resolved and no customer will be left out of pocket as a result of these billing failures.
Mind you, they said that in December - now I'm told they have put extra resources in and are committed to a solution.
The chief executive of RWE npower has welcomed the major competition inquiry into energy firms and said it is "time that the realities of the market were made public."
– Paul Massara, CEO RWE npower
It's time that the realities of the energy market were made public. Britain has the 3rd cheapest gas prices in Europe and the 7th cheapest electricity prices, and we have taken steps to get to the facts as to why bills are going up.
If there are problems they need to be dealt with, and where the market is operating well this can be acknowledged.
Mr Massara added that British consumers deserved a "comprehensive and vigorous investigation" so the public could start trusting energy companies again.
Energy suppliers cannot just blame "old and draughty" houses for rising fuel bills, a leading comparison site has said.
The chief executive of npower earlier claimed gas and electricity prices were rising because British houses waste so much energy.
"The reason why UK energy bills are high is both that the housing stock is not energy efficient but also that suppliers have kept whacking up prices year after year," Mark Todd, co-founder of switching website energyhelpline.com, said.
"Suppliers have raised prices by 140% in the last nine years while users have cut usage. Typical gas usage is down 34% and electricity consumption by 3% and this is in part because many customers can no longer afford to heat their homes.
"The biggest reason for customers cutting usage is unaffordability so without doubt UK homes are now colder than they were in the past. It's crunch time for the energy market and suppliers can't just blame the houses."
Labour's planned freeze on energy prices would hamper investment, the chief executive of npower has said.
"I think it is already having a dramatic effect already. What it's doing is freezing investment," Paul Massard told BBC Radio 4's Today programme.
Mr Massara, who earlier claimed 'Old and draughty houses' were to blame for the UK's rising energy bills, also criticised the Government's plans to reform green levies.
"They made some technical changes on what carbon we actually have to deliver. That reduced the bills by about £53," he said.
"We don't want them to scrap it because actually we think that insulating old people's homes and insulating homes which are leaky is the right thing to do.
"What they should have done is taken all of it into taxation because actually it is unfair that everybody gets hit by the same way in the terms of insulating people's homes."