So I did a lot of messing around with the settings and the only way I was able to get either Advanced Launcher to work or RCB was to modify the program calls slightly to include "--user 0". I am not sure if this is related to my hardware or not as I am using a Minix Neo X7 which was rooted after the fact, but is running their non-root stock rom.
Anyways, for anyone who is having issues and wants to try this just add --user 0 to the commands as exampled below:
start -n com.explusalpha.Snes9xPlus/com.imagine.BaseActivity --user 0 -a android.intent.action.VIEW -eu Uri "file://%rom%"
Thanks for all the work on this one guys, this is awsome!