...tiles on a concrete subfloor? We moved into a newly built concrete condo about 8 months ago. Early on, we noticed that the grout between the tiles is not uniform throughout the condo -- for example, the grout is flush with the tiles in some areas, lower than the tiles in others.

The Developer tells us that this is acceptable under home warranty terms; and that the building is "organic" and it shifts a bit, making it impossible to have an even floor. Adding fresh grout to the low areas is also not recommended: it won't last long, and the colour will not match other unpatched areas.

Is this acceptable, or should we pursue complete repair?

get a complete repair. it is not acceptable. organic? shifts? obviously the foundation was not properly set. if concrete shifts it will crack

Someone got in a hurry !! This is fairly common but I do my best to avoid that in my work. True, that most concrete floors are not perfic and you will have some varience in tile highth. But when the concrete floor is very wavy, a floor leveling compound should be used to avoid this prior to tile installation.
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Also when more than one person is cleaning grout, they can leave different results by one appling more pressure and dragging out more grout than the other.This is probably what happened to your floor.

organic? that is the most ridiculous excuse i've ever heard ...and believe me, i've heard some good ones from my builder! the grout should be a bit lower than the tile and basically uniform. it is not going to be perfect, but it should not be so uneven that it is that noticeable.

If your tile or grout is not cracking you may have a hard time getting it replaced by the builder or subcontractor. Someone else here had mentioned that more than one person was probably cleaning the grout which caused the uneven grout, I believe this may be the case.