I really think it has something to do with their peering, which would directly affect the propagation.
I'd spend some time going further researching the problem (I ran a usenet server plant 1994-96), but I've given the Giganew folks my considered opinion, for what's it's worth. The return emails have been basically 'canned' responses.
As I pointed out in an earlier posting on this thread, I've seen this going on for around 8+ months, comes and goes. This time has been just about the worst. When I first tripped across it this time (several days ago), there were massive 'skips' on a binary group, that, as of today, those parts are STILL not on their server.
But are on every other server I have access to (3-5). I've started moving over to Astraweb, it'll probably take a couple weeks to really test and make up my final mind; the $15/month savings, if Astraweb has no probs (and so far, throughput is 3-4 times FASTER than Giganews, due to them being much closer 'internet wise' to my location) will enter in to it.