I've had the same problem for about 5 years now and unfortunately these are large self tapping screws that backing out if the frame. This is how they chose to secure the floor to the frame.
I originally cut the vinyl flooring in an L shape, removed the screw, filled the hole with liquid nails, reset the screw and then used a vinyl seam seal kit to close up the vinyl. I did this for the first 3 I found but the seam seal does not hold well. Probably operator error :(. Now I just cut a hole in the vinyl the size of the screw head, complete the usual process and seal the hole with a countersunk washer to keep the flooring in place. I have 6 or 7 like this with 3 or 4 more that will be addressed this year. On the bright side, at this rate I will have done them all by next year!:R All I can say is thank god for carpeting, it hides everything.
I thought is was just my Rage'n that had this problem but I'm hearing more about it sad to say.
2008 Phaeton 36QSH