Upgrade to Yosemite failed - MBR and GPT don't match?
This post explains the procedure. Now is probably a good time to make a backup. Then proceed at your own risk...


Get gdisk
In Terminal: sudo gdisk /dev/disk0
Press v to verify your MBR
Press r and then o to list the MBR partition table
Press m and then p to display the GPT partition table information
Compare the numbers for partition 4 from the MBR and GPT tables. The start numbers should match, but the end numbers will probably be off.
Press d to delete the GPT partition 4 (Bootcamp). "Note: this does not delete the actual partition from disk. It only deletes gdisk's in-memory representation of the GPT."
Press n to create a new partition 4 (Bootcamp) using the start and end sector values from the MBR partition 4
Change the name of the new partition 4 to BOOTCAMP
Press v to verify
If no errors occurred: press w to write the new partition table
If errors occurred: press q and try again
Reboot


The important part is step 7 where you sync your GPT and MBR. Note that some of the commands (e.g. disk0, partition 4) may be different in your case. Please adapt them accordingly.