I'd personally choose the grade skip, 100%. The material in first grade may be less boring, and the program should be full day, so she will get a lot more out of the fun aspects of it (social, gym, music, computer, etc.). She's less likely to start hating school that way.
In addition, nothing necessarily rules out entry into the GT program at a later time, or actually the same time. Do you know the cutoff score? Can she qualify based on APR or GPR, or just GPR?
What do you not understand about your daughter's GPR? Just like she was tested, despite being there for only three weeks, other kindergartners were tested too, so she can be ranked against them. Is it the difference from her APR? That's easily explained if she is on the old side for her grade.
