Well, with a bit of searching I've just found a solution to my problem
Same issues, EMPEG wont detect the tuner on occassion.
My voltage goes down to about 10V when cranking. I'm going to upgrade the grounds, but I run a diesel with lots of electrical load at start which is why it sucks.
Have been considering one of those car PSU for mini-itx motherboard which will regulate 12V from anywhere from 6V-30V. Empeg protection in mind.