Thank you so much for your post.
I installed Yosemite 10.10.3 and my Promise Pegasus R4 works just fine. I have to turn off the computer, turn on the Promise Pegasus and start the computer again.
The boot is slower when my R4 is connected, but not so much in comparison to Mavericks (with 10.9.5 I had to reinstall the old Promise Pegasus Kext from 10.9.2 or previous).
The only problem I have is that, strangely, my trackpad doesn't accept 4 fingers gestures when the R4 is connected (1 to 3 fingers gestures works great). Do you have the same issue? I also noticed that after some moments of inactivity, the computer doesn't respond anymore. If YouTube is on, it keeps playing and only audio buttons respond: I have to presso CMD + Shift + Q to log out of the system to make it work again. I already disabled energy saving options.
When the system stops to work it seems that the trackpad is sending the 4 fingers swipe to change the show a different dekstop: very, very slowly my monitor shows this 4 fingers passage to Desktop 2.
My Pegasus R4 was accepted by the system from the start, I didn't have to install any utility. Do you suggest to install last utility and/or any firmware to solve my issues?
My configuration is very simple:
i7 4770K
GA Z87x UD5 TH
16Gb of RAM
GTX 770
It woks fine but I am not sure about the BIOS options.
Thanks for your time!
Update
I installed the last utility software and the situation has not changed. Plus I can't really change the settings of my R4, it seems that the Utility software doesn't connect to my R4 like it used to on my iMac. Maybe because OS X shows the thunderbolt ports as a PCI card.