I discovered a bug (unless already reported). TIM locks up, or refuses to work properly, if it has to look through more then 1 set of connectors. Here is an example:

I have a rover with a 3 cargo containers on it and 2 small reactors. Those reactors are set with TIM to keep some uranium in them. There is a connector on the back of it to connect onto the base and a connector on top to allow my atmos mining ship to dock to it (to manually transfer ores).

The atmos mining ship has a cargo container and 2 small reactors, again, set with TIM to keep some uranium stocked in them.

What I do is I dock the atmos mining ship with the rover, then I drive back to base and dock the rover with the base (leaving the atmos miner still attached).

As soon as the rover docks, my refineries/assembles shut down. As soon as I undock the rover, everything starts right back up. Now, if I dock the rover and undock the atmos miner, everything in my base continues working as intended.

And, yes, all blocks/components/etc are owned by me.