Maybe your BusSpeedkHz value still needs tweaking? From the Clover wiki "If it is slightly incorrect, clock issues may arise and the system will behave in a strange way."
@immo has posted a useful guide on how to calculate the correct value - from post#1:
"Note on mine and other machines you have to manually set the BusSpeedkHz parameter in config.plist as it detects double what it should be, causing animations to go half speed and sound to stutter. I got the number to use by taking my top speed divided by the multiplier when using Chameleon as reported by HWMonitor and then multiply by 1000 (2388/12*1000=199000)."
I tested several speeds, I ended with 199940 as bus speed and 1795 as cpu speed, even with that I got seconds of difference after days but I use a daemon to adjust the clock with ntpdate.
Try replacing your FakeSMC with the attached FakeSMC.kext. I have edited the info.plist so the UsbConnector number for USB ports 1-3 have been set to 3 (normal usb socket) instead of 255 (internal connector). I am also assuming you have EHCI and EHC2 in your dsdt like @immo....
Not really, I edited my DSDT file to change USBx to UHCx+1 and EHCI to EHC1
EDIT: Also I using the same FakeSMC with Mavericks and no problem with icons
EDIT 2: I edited the FakeSMC on El Capitan and set ports 1-3 to 3, now I don’t have internal drive icons on the right or left port. THANKS