I haven't been able to buy any RuneQuest, Traveller, Paranoia, etc, products so far without going online or special ordering through my FLGS. I think it's for two reasons:
1) A lot of shops have difficulty stocking anything they can't sell quickly, so if it isn't d20, it's usually not stocked, and
2) Some of the quality issues that resulted from the self-publishing period put my FLGS off ordering things from them.
In both cases it's a shame, but it just means people have to see the renewed quality and experience demos. If enough people start special ordering, the shops will stock it.