I had same problem and it was cos the windows reformatter on my computer isnt compatiable with some cards. so downlaod this site and reformatt your card again. It fixed my skipping problem 100%
SD Formatter 3.0 (Beta) for SD/SDHC/SDXC - SD Association
I'm pretty sure braj is right. Remember that this phone in stock form has a crap file system and no write cache. So while you are playing music and nothing is going on, no worries. But if an app needs something on disk, like, say, a notification sound....it interrupts the audio stream to play the notification or read/write it's data.
It would be interesting to know of any of you lagfix or voodoo users out there still see this issue?