If polar non-polar intermolecular forces are stronger, why do polar compounds elute first in GC?
I think you're incorrectly remembering something you've been told. People speak of the adage "like-dissolves-like" which really means that polar things interact best with polar things and nonpolar interact best with nonpolar. There are always exceptions and fringe cases, but that adage works pretty well here. Nonpolar molecules interact with other nonpolar molecules pretty much exclusively through dispersion forces. These are the so-called "instantaneous dipoles" you have probably heard of. Polar molecules usually have some way of interacting through dipole-dipole interactions, hydrogen bonding, or simple electrostatics.

Note that the mobile phase, i.e. the carrier gas, does not have a large effect on the retention time in GC, so it really is mostly due to the simplified explanation of intermolecular forces given above.

One might ask why the polar molecules don't also have large dispersion interactions with the stationary phase (they certainly have some), and this is due to two effects. First, polar molecules tend to interact fairly strongly with each other in the gas-phase, and so there is less of an energetic gain for interacting with the stationary phase. This is a problem because interacting with the stationary phase is entropically unfavorable. Second, many polar molecules are smaller than a lot of the nonpolar systems that are studied using GC, and dispersion is correlated with surface area, so the polar molecules tend to have weaker dispersive interactions even ignoring the first point.