Hi there,
I have the same problem. I have an iMac 2010 27" and a MacBook Air Mid 2012.
MacBook Air works perfectly with 10.10.1. FileVault is enabled and never had an issue with any of the updates to Yosemite.
Right now I have that problem with my iMac, it hangs at 50% of the progress after reboot.
With the first update to Yosemite, my iMac worked just fine. Before doing this update, I erase the hard drive and reinstall Mavericks from Internet Install. Then I update to Yosemite and everything was fine. Then, I had the advice from a friend to use FileVault to protect info of the hard drive. So I went home and activated the FileVault encryption. There was when everything started to failed.
The iMac started to run very slow, it took me a lot of time to make any movement on OS. One of the things I remember I did, was to turn off the option of "sleep hard drive" or something like that. And the option of turn off the screen, I configured it to happen after 3 hours. I thought that encryption will take time and I had to be patient. I also thought that if Hard Drives go to sleep often, the process maybe slower, so that is why I turned off this option. Other thing I did, was trying to update to 10.10.1 because I thought that would solve the problem. But I couldn't did it because the system showed an Error when I tried it. So I let go this option.
My iMac was like this like for 3 weeks with no progress in the encryption status bar, in the "System Preferences" window. Was that moment when I decided to turn of FileVault, but it wasn't possible, I had to wait to the encryption progress finish to be able to perform this action. So I searched in some web sites and I found a way to deactivate FileVault from Disk Utility. So I did it and everything came to normal. I was happy.
After that, as I thought everything was normal again, I was happy to be able to update to 10.10.1 finally, so I did it. Worst mistake ever...
First thing I experienced was that the iMac hanged at the gray screen for several hours (more than 24) and the colored spinning wheel. So I decided to erase hard drive and reinstall, anyway I had no much information to lost, everything was manually backed up because I did it when I format the iMac when I had Mavericks.
So I format, reinstall, but nothing happened, now with this issue of the 50% progress status bar. I let it for more than 24 hours but didn't work. Since then I have tried several things like:
Force reboot, but the problem remains.
Erasing/format disk and reinstall Yosemite from USB bootable drive and but the same problem remains.
Tried to Start in Safe Mode, but iMac seems not to recognize Bluetooth Keyboard so Shift function is not available. So I plugged a wireless USB non Mac keyboard, but Shift option still not working.
Tried to start in Safe Mode from Terminal starting from Recovery Mode, but when I hit the command to program start up with Safe Mode, Terminal displays a message telling me that the command wasn't found.
Right now I am repairing disk permissions for the second time (is taking hours) and after that I will try to repair disk, but when I tried to repair disk for the first time, an Error displayed telling me that the disk wasn't able to unmount disk. So, I hope that after repairing disk permissions I will be able to repair disk. After that I will reboot and wait for the best. If it doesn't work, I think I will wait for a new update or reinstall Mavericks or I don't know. I have read that reseting SMC and PRAM works. But I already restart PRAM when I activate FileVault and I think that the SMC option is not available for the iMac. Right now I am very desperate, I have being battling with this problem for almost two months. It is consuming my time at that grade that I am not doing my job.
So, I hope you are reading this, Apple.