I would venture a guess that the pops/skips are issues with the card you are using. you mention battery life with a microdrive, so I'm assuming that that is what you were using when you got the pops/skips. microdrives are not as reliable as CF cards. and with CF cards, you'll want something greater than 40x. several people have reported problems with slower CF cards.
personally, I have made many successful 24 bit recordings via the S/PDIF input, with both v1.1.5 and v1.2.0 firmwares. so I don't think your problem is a firmware issue.