I have the same issue with El Capitan!
MB: Asus H97i-plus
CPU: i5 4670T
Video: HD 4600
M.2 SSD: Transcend 128GB SSD.
2.5" SSD: Samsung 830 64GB.
Memory: 4GBx2
I built this system as the HTPC. At the beginning, I installed Windows 7 Home on M.2 SSD and Yosemite on the Samsung SSD using Legacy boot.
When the El Capitan was released, I wiped out Windows 7 and installed El Capitan on the M.2 SSD and swapped the Samsung SSD with a 2.5" 500GB HD to store data. About two weeks ago, I noticed somehow the boot entries has many duplicated entries for El Capitan. I don't know when they were generated because at that time I only access BIOS when necessary. These duplicated entries were annoying and I changed some of the boot entries to be "Disabled" in the BIOS. After exiting the BIOS, the system stop at the Asus Splash screen forever! I don't know the boot problem might related to my action of changing BIOS. I began to take out all components other than CPU and memory, clear CMOS, changing to other RAM and PSU. The board was just dead. I contacted Asus and asked for RMA.
While I am waiting for the RMA instructions from Asus, I found a fair deal in Amazon for a used Asus Z97i-plus and I just bought it. After couple days, once I received it, I moved all components to Z97i-plus and it booted to El Capitan right away. Well, since there are still some problems of El Capitan installation like Wireless/Bluetooth, USB issues, I decide to move on and figure out how to fix them.
But there is a big issue with M.2 SSD. Whenever config.plist in EFI parition is modified, there is a chance the OS X might fail to boot. Because the M.2 SSD is located at the back of the motherboard and won't be able to take out easily for any modification with another MAC (I do have another system running OS X and Windows 7). The easy way is to install another copy on the regular HD. Therefore, I installed El Capitan on a small partition of the regular HD. In that case, whenever I want to try any new fix, I will go to BIOS to select my HD to boot and modify the config.plist on the EFI partition of HD. If the updated config.plist causes any issue, I went to BIOS and selected the SSD to be the boot drive and booted to OS X on SSD. After that, I can roll back or modify the config.plist on the EFI partition of HD easily. BUT I began to pay attention on those duplicated boot entries in the BIOS since I have to go to BIOS to select the boot drive.
Suddenly I found system stops at the splash screen again! That really scared me to death! This time, I just removed out the HD and clear the CMOS. After that, it works fine again.
After a while, some of my memory came back regarding to my last action before my H97i-plus was dead. I wonder they might be related. My guess is, Asus BIOS has some bugs and corrupted the NVRAM after I changed the duplicated boot entries to be Disable.
The strange thing is, I found most of duplicated entries are for my M.2 SSD (more than 8-10) and there are always three entries for the regular HD. I installed El Capital with Clover once on Asus H97i-plus. Then I moved the M.2 SSD to Z97i-plus and installed El capital on the regular HD. I still don't know how the boot entries grow and when Clover wrote boot entries into NVRAM after spending almost one day to google. Any one has answer? Is Clover or EFI BIOS that inserts those boot entries into NVRAM?
It seems there is a number limitation regarding to these boot entries in the BIOS and the board will stop at the splash screen once it is hit!
Now I pull out the M.2 SSD and only keep HD for study purpose. I won't put back the M.2 SSD before I got the answer!
Update:
I just saw a post here regarding to this issue. It will tell you how to fix this issue. But it seems that is caused by Clover and so far there is no solution for a system with more than one EFI partitions.
