I've never had a problem with a Region 1 DVD, but certain Region 3s give Clone mobile problems (they're the same ones that give PocketDivx problems.) For example--I just picked up the Hong Kong version of Midnight Sun, and you can select the subs--Clone understands they're there--but then they don't show up in the final product. I tried using DVD Shrink to make a copy with only the English subs available, and then have Clone work on that, but still no go. I'm not really sure what the distinction is, some stuff always works (any Celestial or Joy Sales release) and then other stuff doesn't.
If anybody from Slysoft reads this and feels like picking up a DVD to try and reverse engineer what's going on--here are some DVDs that I can't get subs to appear on:
Midnight Sun (see above)
Murder Take One (Hong Kong version; I can get the Chinese subs to appear but not the English ones; even when I select the English ones only the Chinese appear)
Dasepo Naughty Girls (Korean release; same thing as above, you can get the Korean subs to appear but not the English ones)
There's others, but I'm blanking at the moment.