The only suggestion I have is do not install rEFIt; if you did, you might have to erase the partition and reinstall Lion. Follow instructions here
except run Partition Inspector by itself without installing rEFIt.
I think I have the same problem. I have a late 2011 MacBook Pro with Lion and Boot Camp (Windows 7). I had no problems rEFIt 0.14 even after I added more partitions after the Boot Camp partition by using a Parted Live CD and updating the MBR with rEFIt.
But, that all that fun ended when I replaced the orginal hard drive with a Seagate hybrid drive. I ended up with the problem of having the Mac hang whiling booting into Lion. To boot Lion, I have to hold down the option key right after the computer reboots or boots, and select the Lion OS partition ("Macintosh HD"), and even then the system hangs after one successful boot, and causes minor damage to the file system.
I erased the drive and reinstalled Lion. Everything goes will until I reboot after installing rEFIt. Follow rEFIt's removal instructions in the readme file does not fix anything in this case.