Okay, so I don't know if this is related to #338, and/or my previous report #232, but this one seems to be more severe than either of those — it involves the unloaded ship losing all RemoteTech capabilties altogether, not just the status as a command base.

Sequence of events:

1. Fire up KSP, load savegame, tracking station, open my space station
2. Build and launch a new unmanned ship using ExtraPlanetaryLaunchpads
3. Pilot that ship until I get far enough from the station for it to unload
4. Station is no longer transmitting whatsoever — no red dot, no communications lines

Other notes:

• RemoteTech 1.6.3 from CKAN (verified in logfile), which, to my understanding, includes fixes for both the above issues
• doesn't happen if I load the station and then switch to another ship
• doesn't happen if I load the station, build a new ship, and then switch to another ship
• log is being spammed with "-1" over and over, but I have no idea what mod is doing that
• no mention of "GetInt" in the log

Files:

• KSP.log: https://dl.dropboxusercontent.com/u/32378574/remotetech-unload-KSP-log.zip
• Savefile after testing: https://dl.dropboxusercontent.com/u/32378574/remotetech-unload-KSP-sfs.zip
• Video of reproducing bug (producing files above): http://youtu.be/I0jiufszGsI (sorry, my voice is very quiet and ShadowPlay was being stupid with the push-to-talk)
• Craft I was testing with: https://dl.dropboxusercontent.com/u/32378574/remotetech-unload-KSP-crafts.zip

Let me know if you need anything else. It's not a huge problem for me right now since I can just switch back to the station and back to my ship again if necessary.