Not sure I can see the first picture too well.

Any chance you can shoot it in better light?

The time to address this issue is now for certain. There should also be sheathing on the sides that the flashing is attached to.

Here are some photos I took this morning.

There are several possibilities:
1. The windows was mis-ordered.
2. The framers framed the opening too large.
3. The manufacturer's maximum height was reached and the windows couldn't be any taller. If this is the case, the supplier should have notified you.

Why would windows be installed before the sheathing? I'm not a window pro, but I have built a couple of houses and your install does not look correct (I could be wrong). The window opening with the gap{{gwi:807}} should have had a shim added to close the gap, prior to installing the window. See the link below on new construction installation.

Here is a link that might be useful: link on window installation for new construction

This post was edited by lkbum on Tue, Feb 5, 13 at 14:42

I will let the pro's who know installs better than I handle this further but I am afraid of most of what I see there. No sheathing, no shims, no drip cap, window wrap should extend into the opening and wrapped onto interior of the studs, looks to be nailed only through the flanges (can't really tell 100% but looks that way to me).

+1 to ultra's comments.
At this point, if the size of the windows is satisfactory, those openings need to be closed in. Nothing too terribly difficult, but it should have been done prior to the windows being installed, along with a few other steps as mentioned above.

+2

I would just frame it up a bit.

The issues with the sheathing and the other items are a bit off putting to me though.

Thanks! I really appreciate it.

I will talk to my builder about this.