I figured out this is happening because the way my limit switches are wired in series with the E-stop circuit. This way it kills everything if a limit is hit (could be bad if the computer loses it's mind).
I also have a an input tied to this for the limits. This is being held at 24V until Mach fires up, then it goes low like expected.
This is also likely what is causing my E-stop messages at boot.
Not really sure what I can do to fix these from not happening. The E-stop circuitry is on the Machmotion IO6 BoB (originally designed for Mach3 I guess).
It's working fine, but these false messages at boot are annoying and if I don't use the machine for awhile and forget, I will be wondering why it is happening again, or if someone else ever used it, they would think there is a problem.