What recovery are you using? Many people are reporting that ClockworkMod seems to have trouble with ROMs using the 3.0 kernel, making them unbootable even on a stock boot layout. TWRP doesn't have issues with it, so I would try that if you're currently using CWM.
If that's not the issue, then try using the "/dev/block/mmcblk0p#" style to specify the partitions in the updater-script. I had some difficulty getting it to play nicely with the "by-name" style for whatever reason, especially with the boot images (I'm not really sure why, though).
Got an Android question? Stop by Android Enthusiasts!