There is noticeable flexing and squeaking the fiberglass shower floor of my newly constructed townhouse (3rd floor bathroom). The drain cover also does not sit quite level and I am quite concerned about what problems this may lead to in the future. I just moved in and so have yet to do my 90 day or 1 year punch list. Should I be pushing for this issue to be resolved or is it just a nuisance that I should live with ? I have never experience this kind of problem within the shower before and at least case, don't like the fact that there seems to be some problem waiting to get worse eventually.
There is also some badly set tile on the tub deck next to this shower partially due to the front wall having some bow in it. Lots of unlevelness and attempt to make the tile fit a non flat surface. What can be done to allow the tile to be set correctly and have a level/flat appearance ? Anything short of rebuilding the tub deck front wall with straight lumber ? Thought there maybe some leveling techniques that experiences tilers would use.

Thanks for the help on these 2 issues as they are the only serious ones (to my knowledge) in my new house and I would like to be armed with information before pursing this further with my builder/contractor as I do not want to end up with problems after out of warranty.

And you signed off and closed on this unit? Expect leaks from your shower in the near future. The shower floor should have been bedded at installation.
Also expect leaks from the tile wall if you use the shower while in the tub. The tile grout will shrink away from the uneven tiles and leave a gap where the water from shower splash could enter. You should go over this with your contractor soonest. The tub wall should come out and be rebuilt and the shower floor should be bedded and supported so that there's no give when you step into it. Good luck, Tom