Kerbal Space Program

Reproduction steps:
1) select custom flag (at the flagpole)
2) restart the game & load the save
3) go straight to the VAB (or SPH)
4) launch something from there
5) there will be the default flag near the pad and at the astronaut complex

Other observations:
1) the same effect happens if the first action is activating a craft already at KSC
2) Switching to KSC view and back to the craft usually fixes it
3) it doesn't happen if you quit to main menu and load the save again or switch to another (most likely, it happens only the first time you load a save after starting the game)
4) behavior of flags in KSC view seems a bit inconsistent - sometimes they look right from the start (even if the glitch happens when you launch the craft), sometimes they also are reset initially

Probably the first time KSC view is initiated some flag assigning script runs before the relevant objects are fully loaded (or is overridden by another script). However, I found no error messages in the log.

I'm attaching a save with a red flag (rings) selected and a rover near the flag pole