Okay, so I just ran into a variation of this problem and since this is the top search result I figured I'd add my observations for my particular problem. In my case it turned out that the reason the boot helper partition couldn't be updated was because both the Recovery Partition and my main OS were attempting to update the wrong boot helper partition. In my case this meant that I could only boot my computer in Safe Mode; booting normally would get to just before the login window would appear (or for FileVault users before your desktop appears) at which point it got stuck and wouldn't continue.
For those that don't know, every Mac formatted disk should have a partition scheme that will include an EFI partition, and also a partition called "Boot OS X", however in the case of your main disk the "Recovery HD" partition will fulfill this function instead. You won't normally see these in Disk Utility unless you enable the debug menu (I used Cocktail to do this, but there are Terminal commands available as well) and tell it to display all partitions, or you can use the Terminal command "diskutil list" to view all partitions.
While booted in Safe Mode I noticed the cause of the problem was that I had a mounted Boot OS X volume on my Time Machine drive after trying to set my startup disk. So I unmounted it, and mounted my Recovery HD partition instead. Unfortunately at this point Startup Disk still gave the same complaint by choosing the wrong partition. However, I was then able to use the following command to correct the problem:
sudo bless --folder=/System/Library/CoreServices --file=/System/Library/CoreServices/boot.efi --setBoot
I could then restart normally and login and everything… true luxury living!
Unfortunately for people that need to switch startup disks regularly this probably won't help; I can't for the life of me figure out why Startup Disk is insisting on picking the wrong boot volume. It's a pretty serious bug too as it means that the OS X installer won't work either when running it from the Recovery Partition (I thought I would need to do that to fix my system, should have tried Safe Boot first) since it needs to install something into the boot helper partition.