aakk9999, thanks for that. When I change the filter, the numbers for individual keywords now match up. Total impressions are still off (higher in WMT than GA), but I'm not really concerned with them, anyway. Also, those keywords I couldn't find in WMT now show up.
Actually, it brings up something I need to look into more. One of the weirder keywords is showing up as image, even though we don't actually get much image traffic usually, as our images are hosted on a CDN.