The Autom8 windows appears to fail after "too much" output, where "too much" is in the scores to hundreds of lines range. This makes writing and debugging Autom8 lua scripts very difficult. The failure takes the form of a lack of further output being printed.
To replicate, try running the help() functions repeatedly from any of the Simple*OrbitalMechanics scripts from Post #53 in the Mechjeb Autom8 megathread.