Okay, I'm figuring out more of the filtering process. Apparently, only emails that are :
1. In your Inbox
AND
2. In your S:Waiting On label
show up when you look for "waiting on" because only those are actionable at that time. Makes sense, but still confusing, and problematic, because i like to push emails out of the inbox and if I do that, they won't show up in "Waiting On". That's silly to me. Oh well, if this continues to be as annoying as it has been, I'll uninstall GTD Gmail and just use the old fashioned S:, R:, C:, P: prefixes before the original gmail labels. GTD GMail CAN do a lot and has a lot of features, but it seems like there's a lot of specifics on how you must do your email. I'll have to read up on it a bit more.