Restart the game. Saints Row games are buggy with displaying messages and the HUD. Stuff like that simply happens for no rhyme or reason and it's often not a mod that causes it. In most cases a restart will fix. I would be interested if you can reproduce it after a restart.
My apologies to you for having wasted your time! I could have sworn I had restarted the game; but, in hindsight (happened early this morinng), I guess I just reloaded a savegame, instead (and the problem persisted).
Anyway, the problem is conpletely gone now after a restart.

The problem persists, and is *reproducible* -- I just didn't realize the proper conditions under which the error occurs. Everything goes well when I simply 'continue' on startup. But as soon as I load a savegame (*any*), I get the persistent 'store this vehicle in your garage' message again upon entering the heli-pad garage.