It will look fine. Most of the new builds in my area use the clay/tan vinyl windows also. My remodel we bucked the trend and have white windows with white wood work. The link below is from a builder in our area with clay windows with white trim and it looks nice. If I had a choice I would choose white in a new build.

I think the clay trend is more for the exterior appearance than interior.

http://www.nieshomes.com/2216flutter.html

We had (and still have in the bedrooms) beige windows with white trim. I don't like it at all. Everyday I curse the person who decided beige windows would be better than white for this house. During our whole house reno, we removed a couple of windows and added some new ones in the main part of the house and i ordered them all in white. I made sure we had enough in the budget to replace the one beige window left in that area of the house. Unfortunately, we didn't have enough money to replace all the windows in the house so the bedrooms stayed beige. Replacing those is on my radar for a some-day project.

That said, if you're stuck with the clay windows, ignore them and do what you want with the cabs. I wouldn't let the window color sway me from my love for white cabs!

During our build, my realtor said white windows were cheap looking (since it was standard here in low-price builds) and beige was a custom/better option. I had too many other details to obsess about and we got the almond/beige/whatever windows. From the outside of our house, which is a sandy stucco, it looks cohesive and beautiful. However, from the inside with all our white trim and cabinetry, I still resent listening to the realtor. I think it would look better all white inside. With that said, it doesn't look bad..... (it's just not my ideal.)