I had a similar problem and it relates to Clover giving preference to the last booted volume recorded in NVRAM over the default boot volume specified in the config.plist. I fixed it using the latest Clover r2652 to IgnoreNVRAMBoot and also setting the EFI as the Default Boot Volume.
- Delete your current NVRAM settings...in terminal
sudo rm /nvram.plist sudo nvram -c
- Place ntfs.efi in EFI/CLOVER/drivers64UEFI
- Edit your config.plist, entering the Default Boot Volume as EFI and ticking IgnoreNVRAMBoot with Clover Configurator...
- With the correct config.plist settings, everything works as expected (including timeout countdown!)....
Of course for legacy Windows, the Default Boot Volume would usually be "System Reserved".Go to the full post