Problem with hard drive in startup

Working with MacPro (early 2008) Processor 2x2.8 GHz Quad-Core Intel Xeon, with memory of 28GB 800 MHz DDR2 FB-DIMM, I have operation system 10.6 run on hard drive #1 with storage on #2 and installed operation 10.10 running on hard drive #3 with storage on #4, each drive is 1TB in size. What i want to do is in System Preference under startup disk is switch from one to the other based on what i'm working on. The problem is that it has been working but what happens is sometime drive #3 doesn't show up, only drive #1 is shown. I then must redo all the work again an install #3 operation system. What am I missing?