The GEE algorithm is an iterative algorithm that solves for both the parameter estimates and the covariance matrix so you should expect to see differences in both the parameters and the standard errors. There will be more specific details here http://support.sas.com/documentation/cdl/en/statug/68162/HTML/default/viewer.htm#statug_genmod_details29.htm   ... View more

Sorry I can't help more regarding correct SE methods. As I'm sure you know, most resources I found in internet searches are directed specifically toward complex sampling schemes, not unequal weighting problems exclusively. How different are the errors between MEANS and SURVEYMEANS? If you don't have complex sampling design, they should be pretty similar. Also check your weights for extreme values as this can be problematic. An alternative is to calculate stabilized weights, which usually reduces standard errors. Good luck. ... View more

  Control sorting in PROC SURVEYSELECT would get you a match to the population frequency, if your population has the right size.   STRATA would let you select certain numbers in each stratum, but it sounds like you're really not going for that detail (that would be 1:N).   You could use pre-sampling weights perhaps with the SIZE option in SURVEYSELECT, to weight your control population to match the demographics of your experimental group? ... View more