In my experience with a failing controller, that yellow flashing light indicates an SD card error...or a USB error...it was never quite clear.
I too suffered through the vagaries of the controller, so I feel your pain. I've had "better" luck with the replacement controller, but like you're finding, it's not 100% reliable.
The good news is that sometimes it's not the controller...just yesterday Vectric VCarve Pro v8.010 took a millimeters design with 5mm safe height, and when I changed it to inches, it KEPT the "5" and turned that into 5 INCHES safe height. So when the GCode was run, it's first action was to rapid all the way to the top (and then some!), and then immediately RAPID plunged an 1/8" solid carbide endmill through a 3/8" plate of aluminum, and broke the endmill, and made that $25 plate of Aluminum useless. Thanks, Vectric.
Thom