My guess is that 6.0 isn't supported due to there not being any official development thread for 6.0 on our S4's. Marshmallow is pretty new and probably won't reach the S4 for a few months (as did TW lollipop) Have you tried installing the CM13 as primary, or even without multirom altogether?
i can confirm this issue:
installed CM12.1 Antares optimized as Primary and different Roms as secondary: crdroid, CM11, SlimSaber, Antares CM12.1 Test.
Everytime i choose any secondary Rom, it boots to TWRP instead of booting into Rom.
Selection Reboot in TWRP boots into selected secondary.
Then after it booted into recovery I selected "reboot system" as Michael mentioned said and it worked.
Will give it a try with CM13 today and report back.
EDIT: Does not work. FC on boot.
CM13 seems not to work as secondary. Might work as primary but I did not try.