My system has 3 OS versions installed in three different drives and partitions. Prior to the upgrade t0 10.11 (of one of the three) all three booted correctly. Now after the upgrade, the other two partitions do not boot and instead it goes back to 10.11.
I have OS X 10.9.5 on the first disk and partition, 10.11 on the second, and 10.10.4 on the third. The system has 4 total drives, the 4th being used for TimeMachine. The 10.11 partition is on the internal drive. THe other two on removeable USB drives from WD.
Anyone else seeing this?