I have a persistent problem on my 2005 Giant Trance, nasty grating chain skip. I've replaced chain/cassette/rear mech (chainset is reasonably new and not very worn), but this hasn't fixed it. Seems to do it in any gear.
I'm wondering if it might be skipping around with suspension movement, but it's hard to figure that out. It often makes a nasty clatter when I start pedalling again after a bit of freewheeling over obstacles. I've re-routed the rear mech cable down the down tube and zip tied to the swingarm linkage, that didn't work either.
Interestingly, riding at the weekend it was really bad for a while then after a dose of wet/mud, seemed to get better. Chain too clean???