Turning off the computer for the night seems to be causing the problem. It seems that rEFInd can not load the bootmgfw.efi file and it hangs on a black screen until reboot. The screen is all black and simply says: Starting bootmgfw.efi Using loading options ".
Loading linux after a dark night works very well. Restarting my computer also allows me to boot Windows, going through the previously failed boot process.
I have reinstalled rEFInd but I still have these problems. Any help would be appreciated.