This, in fact, is probably related to all logic devices built on "machine base" and #71 is probably a part of the issue. The GUI in at least counters, logic, ender monitors, power monitors and sequencers is in default state after the server has been restarted, although actual config is loaded and devices are working. Breaking such device and placing it again shows the actual config. Some init missing? Tested on Forge 36.2.5.