I had that same problem. I had Windows 8.1 and Linux in Legacy boot mode and when I installed via MultiBeast (which I created as UEFI) I tried installing through UEFI. The way I fixed it was to Select LEGACY as the Bootloader in MultiBeast. Once it was working, with CSM enabled, obviously, I had to turn off CSM and enter Clover UEFI Shell to delete the MAC OSX entry from the boot list. I then re-enabled CSM and the MAC OSX entry was no longer on the boot list and I was able to boot normally.
Maybe there should be elucidation in the Installation instructions. Basically, before starting the OSX installation, if you have an OS already on the PC and it was created as UEFI then all subsequent OSes have to be installed in UEFI because the UEFI EFI boot file is located only on that one drive and it writes the disc drive selection to the mobo's NVRAM.
If, however, one has already installed an OS, say Windows, in non-UEFI (there won't be a EFI directory on the disc) then all subsequent OSes should be installed as Legacy.
If you install all the OSes as UEFI then you can use Clover as your bootloader to boot into any other drive. The problem is that if Windows decides to update the boot file it will probably erase the other drives boot entries. (Heck, it did it to me (Windows 10 upgrade) and it wasn't even in UEFI mode, but it did scan all the drives and deleted my Linux GRUB2 bootloader (which I had to repair & re-install) and created an Apple folder in the third disc drive that contains OSX which seemingly has no affect.)
So, even though the Install instructions say to use UEFI if you have a Z97 or Z170, for example, which are UEFI mobos, you will want to install in Legacy instead if you already have another OS that was installed in Legacy. You will then need to use the BIOS boot F key to select which disc to boot, and/or you will need to add the other discs to the disc boot loader. (For example, I installed Windows (not knowing that I could have installed it through UEFI, so it installed as Legacy) and when I installed Linux it automatically added Windows as a boot device in the GRUB bootloader.)
You may want to try re-installing through UniBeast, making sure that you completely erase the hard disc, then when you run MultiBeast select Legacy as the boot loader. Or you can create another UniBeast USB installation stick, but this time selecting Legacy as the bootloader. Just buy a brand new 16GB stick since having two UniBeast sticks doesn't hurt. I find that one can use a UEFI-USB UniBeast and so long as CSM was enabled when it was installed when you run MultiBeast and select Legacy it, in all probability, will allow OSX to boot normally. ymmv.
