Yep this is pretty common. If it goes more than 10 or 15 minutes i'd say it was a bad flash, pull the battery and try again... ran into that once or twice. The JB bootloader does help, as well as using the nexus super wipe script plus manually wiping system/cache/dalvik directories manually.
It was crazy the first JB rom I flashed it booted (first boot) in under a minute and was flawless, every other one takes 5+
Don't sweat it, its a JB thing... it takes time to load all the awesome