I am no expert, in fact I am a FTM and struggling with the naps of a 4.5 month old. However I wanted to pass some information that I got by taking to a sleep consultant how does research in sleep. My baby was having the same sort of issues you are describing. All of a sudden he started with 45 min naps at around 3 months. I tried extending and shortening the a time, to no avail. I tried all sorts of things. The only thing that worked for me was to soothe him back to sleep once he is done with that first cycle. I pick him up from the crib and shush him, bounce him, pace him and give it a good try (of 15-20 min) to help him fall back asleep. Tracy would probably disagree with this tecnique, but the shush-pat method has never helped me bridge the two cycles. Most of the time it works and he is able to fall back to sleep for another 40-45 minutes, sometimes I can't get him to fall asleep. When I told this to the sleep consultant she said it was very normal for babies to not sleep more than 45 minutes before they are 5 months old, when they start learning how to bridge the two cycles. So even if he wakes up and seems rested after 45 minutes, I can tell he needed more sleep if he can fall asleep in the next 15min.
I have noticed too that keeping him in a dark room helps because that way he is not as distracted when he comes out of the first cycle and call fall asleep back again. I transfer him back to the crib when I am absolutely sure is is deeply asleep, otherwise the little rest he had is enough for him to fight that second cycle.
If you want more information you can look at the webinars for free at
http://www.isisparenting.com/page/webinarssleepit is the last one titled: The Science of Infant & Toddler Sleep presented by Isis Parenting Sleep Team Leader & Senior Sleep Consultant and Harvard Medical School Sleep Researcher Dr. Erin Flynn-Evans, PhD ALM RPSGT
A few times has my baby been sleeping more than the 45 minutes, so I am still waiting for him to hit the 5 month mark and possibly beyond when he can do it by himself.
Good luck and I hope you figure things out