I've never heard of sugars being cooked so long they become less fermentable. Not saying it can't happen, but I suppose it is possible to damage or otherwise reduce the nutrient content of the malt to the extent it becomes less fermentable or at least more of a challenge for your yeast...?
That being said; I'd have to say it is more likely that your yeast is simply exhausted. Even if the pitch rate was dead-on, nutrient or oxygen deficiencies can easily lead to a stuck fermentation with high-gravity brews.
Did you aerate your wort sufficiently prior to pitching? And possibly again at 12-18 hours? An aquarium pump, filter, and a sintered stone would be useful for this task. For higher-gravity beers, oxygen is key to a good full fermentation. In a pinch; you could always pitch a small starter of a clean yeast (such as WLP001) at high krausen to restart fermentation and finish this one out.
You mention it is currently in the secondary. Did you take an SG reading prior to racking off the yeast cake? Pulling too soon w/o confirming fermentation is complete will leave too little yeast to finish the job effectively, as well as not allowing the yeast sufficient time on the cake to clean up after itself. Just a thought.
