Very useful tips, big thanks!
I had the same problem as above and Clover did not even install onto the HD. I followed the above guideline (had to reboot, though), but finally not I have a perfect system.
Actually I had a very similar problem after installing El Capitan. Furthermore Clover install was not successful (without error, but did not work).
Following the above tip helped, logical volumes and extra volumes in Clover disappeared and Clover did install on the HD just fine.
This is so cool... I have a G41MT-D3V motherboard (should be very similar to yours) and currently running 10.10.5 with Chameleon.I think I will try to upgrade this to El Capitan and Clover this weekend...
EDIT: So far I have made a clean (Clover) install of Yosemite then upgrade to 10.10.5...
I have not done an upgrade hence I am sure that my advise would not be the best. Sorry, but better to be honest.
Also since I am abroad at the moment, I still need to upgrade to 10.9.3, so can not comment on that one either.
While it is not exactly the same mobo, but very similar:
I have also installed Maverick on one computer with this motherboard, and worked absolutely...