I had this problem for a while now. (No idea if it's just my RW or is it a thing with custom slugcats)
My slugcat's timeline is based on Rivulet's timeline and connection dots between rooms in region don't appear for UW, SH, SB.
I assume it's because of SH_E04RIV, UW_A11RIV, SB_GOR02RIV and all other Rivulet exclusive rooms in those regions (or map for this timeline. I tried changing timeline base to "Red" and connection dots appeared in SH&UW, but then I have wrong map.)
I also get same issue when trying to add my slugcat specific map files for regions where dots appeared fine before. (and doing this for UW, SH, SB doesn't fix issue)

I tried going in SB with different custom slugcat that has it's timeline based on Saint's&Rivulet's timeline and connection dots were also missing for me.

Biggest problem is that you can't see all rooms in region on map without connection dots. (Unless it's your current room or it's close enough to you to be visible)

Is there any way to make them appear?