You may want to look into that agena contract because I had the same issue as bluemoon. The JR docking port wasn't recognized and I ended up comping the contract via the debug menu.

Also, if i could make a suggestion. The skylab contract requires very specific parts. Unfortunately, the stock part revamp mod replaced the required solar panel with a different named part So the only way I can complete it is to comp it manually once I've completed it (in spirit anyways).

Perhaps having its criteria being the solar module instead instead of a specific named part might be a better alternative? The same could be said of the science lab module so mod science labs could count. Anyways, just a thought.

I tried to mod the mission config for my personal use but couldn't find it. Did you move away from config files for the missions?

Not sure why this is not working. It should. Will have to do more testing.

Possibly have fixed this. Was an issue with module only can be completed while on launch pad. If player switches vessel while in space the Completed objective goes back to red, and can no longer be completed when you come back to vessel.

Hopefully this fixes the issue.