There was the €65m deficit, the loss of the English Premier League, the drop in advertising funds, Pat Kenny quitting to join rival station Newstalk, and ever increasing competition from US and UK channels.
"It has been tough," managing director of television, Glen Killane admits.
"There have been losses and cuts. There is still a huge mountain to climb, but we're getting there."
Glen (41) began working at RTE in his early 20s, after his dreams of becoming a globetrotting news reporter fell through.
"I did an MA in Journalism, and had designs on being a foreign correspondent," he explains.
"I was about to go Mexico and write for a newspaper there but it fell apart for very long and convoluted reasons involving a Mexican president getting impeached."
"So instead I ended up in RTE's sports department. I never envisioned producing sport or working in TV -- it was sort of a happy accident."
After several years editing and producing packages covering GAA matches and the All Ireland finals, Glen moved to ITV to work on their ill-fated Sports Digital channel.
"It was like a mini university of sports production. It was a great training ground.
"Plus, I was the lead editor on live football so I got to see such wonderful places as Grimsby and Stockport and Burley village," he says dryly.
Glen returned from the UK and in 2004 was appointed head of RTE's Sports Department.
Given his background in sport, the loss of the Premier League was a particularly difficult pill for him to swallow.
"No one would willingly give up the Premier League, but it was a case of 'What's next in line?' There is no low-hanging fruit left when you have cut the amount we have cut.
"None of those decisions are easy. There have been losses," he says.
"We have taken over €100m a year out of our operating costs.
"To make that possible certain things had to go and the Premier League was one of those things. It was an extremely resource-intensive show."
But after six years Glen decided it was time to move on from sport.
"The opportunity came up as MD of TV; you get to that stage where you think is there more you could contribute. I felt it was time to let someone else take on sport."
In the past three years, Glen has been integral in deciding what hits our TV screens and the re-vamping of the station's internal structure; there are now newly appointed channel controllers and "genre heads".
Predictably, the overhaul caused a stir within RTE -- roles and positions within the station changed.
Former director of programmes Steve Carson was perceived to have lost out when the channel controller positions went to George Dixon (RTE One) and Bill Malone (RTE 2).
Shortly after the respective appointments, Carson (45) left the station to join BBC Northern Ireland.
It may seem like a strange move, given that his wife -- Miriam O'Callaghan -- and children will still be based in the Republic.
But Glen is adamant that there is no bad blood.
"Steve got a very good offer from BBC Northern Ireland and it is as simple as that. He is a big loss to us but there is certainly no personal agenda," he says firmly.
"We have restructured. But that had nothing to do with Steve. That was to do with the challenges we faced as an organisation.
"There was no issue around making Steve redundant -- his job simply evolved; everyone's job did."
In the past few years, there have been several success stories for Glen: the launch of RTE Junior, hard-hitting documentaries such as The Disappeared, and the overwhelming success of gangland drama Love/Hate.
With sky-high viewing figures and the rights being sold internationally, it would be easy for RTE to keep trotting Love/Hate out, but Glen insists the series has a natural sell-by date.
"We won't be throwing in extra episodes or tacking an alternative ending on for the sake of it.
"There is a story arch that goes to a set number of series; head of drama Jane Gogan is certain about that.
"Sometimes it's good to walk away from something on a high before it starts to peter or fizzle out. Not that Love/Hate is in danger of that," he adds quickly.
In the future, Glen says there will be more drama on RTE2. "I'd love to see a return to the days of Bachelor's Walk," he says. There's also a push for fresh presenting talent and comedy output.
"Comedy is a big area for us. Not so long ago RTE was considered a bit of joke when it came to comedy -- and not in a good way," he said.
"We weren't developing comedy but I think that has begun to change if you look at Damo and Ivor, Mario Rosenstock, The Savage Eye and Republic of Telly.
"When you're a small country sandwiched between two of the greatest producers of English language TV in the world -- namely the UK and the US -- there is a danger you may be swallowed up somewhere between Cumbria and North Dakota.
"We're not a region of the UK or US, we are Ireland and RTE is about reflecting that and looking at the world from a distinct Irish perspective.
"That's what we're here for," he says.