I had the same problem with a Pale Ale I made a few weeks ago. Everyone told me to invert the bottles a few times and store it in a warmer place which I did and its still flat.
I'm thinking along the same lines as you are about the "did it stay in secondary for too long" line of reasoning.
I think I let the beer sit in secondary too long, and in fact I'm almost sure thats what happend now that I've had a chance to review.
Gotta keep in mind that most of these people here who advocate leaving the beer in the secondary for a long time probably keg their beer instead of bottling it anyway.
So far of all the beers I've done ( getting close to 20 batches now ) the ones that were in secondary the longest are the most carbonation challenged. And the ones that I bottled right out of the primary and let condition in the bottles instead came out the most nicely carbonated.
I think from now on if I'm going to bottle beer its going to get 1 week in the primary 1 week in the secondary, or maybe even just 2 weeks in the primary.
I'll save the long stays in the secondary for when I can put a beer in a keg and force carbonate it.
This is just my take on it, I'm no expert but I think if you bottle your beer and you want it carbonated like a commercial beer then you're better off letting the beer condition in the bottle instead of in the secondary. Well at least don't let it sit in the secondary for too long.