What is the mechanism behind time perception?
There are several mechanisms for time perception that depend on the task performed (counting, judging prospectively, retrospectively) as well as on the duration of the interval to be judged (duration perception for 1s intervals works differently from 1minute or 1 year). Overall the idea you advance of multiple mechanisms is well accepted. This is just a link to an article just published on the matter.  

http://www.scientificamerican.com/article.cfm?id=your-brain-has-two-clocks&amp;utm_source=feedburner&amp;utm_medium=feed&amp;utm_campaign=Feed%3A+sciam%2Fpsychology+%28Topic%3A+Psychology%29

Perhaps if you could be more precise in your question and restrict your domain it will be much easier to answer about the neural foundations you are looking for