Not likely but have to ask - what does your CPU and memory utilization look like when the skips happen? (System/Administration/System Monitor tab)
If I remember correctly a "real-time OS" only guarantees that an interrupt request will be responded to within a minimum time, not that it will be completed in a minimum time. The completion depends on CPU and RAM and IO resources being available. While most mp3 players have tiny resource footprints it's not impossible to have problems if you're on an older machine. I've induced similar symptoms when running Windows under a VM with very limited resources.
More likely - the symptoms could be caused by the decompression of the sound track failing. I'd be tempted to remove and re-install whatever decoder you're using. Ubuntu 10.4 is capable of reasonably good sound on most systems so don't give up without a fight.
Added: Based on the DROP in CPU use I'd guess either the IO system is unable to fill the decoder input buffer or the decoder is bailing out unexpectedly. Does the problem happen with all CODECs? ie, can you play a .wav file ok but not a .mp3?
The HD on RAID0 (striping) makes me wonder if that could be relevant. Maybe the RAID0 is grabbing the bus a little longer than it should be. Does the problem happen at regular intervals? What is the interval (on average) if not regular. Can you play OEM CDs? Can you play mp3 from CD? Can you make a RAMDISK and play from there? If any of these work without skipping it will shed some light on whether the codec is the problem.
I'm assuming you use the Update Manager to get regular updates. If you haven't done this for a while then do it now. If it grabs any new stuff be sure to verify you still have a problem before proceeding.
How to reinstall decoder(s) - I'd hold off till "last resort" to do this... but if you're still reading then here's how:
It depends on the type of file your playing. This example is for mp3... you'll have to find the decoders in use. Run Pkg Manager then search for mp3. On left hand side click STATUS and pick "Installed". In the list of matched items - on left side the decoders in use will have a solid green box and something about mp3 and decode in the title. For example on my system one file is libmad0, the "MPEG audio decoder library". Record the names you find so you can add them back later. Right click and "mark for removal". Repeat until you're satisfied you've got the main items where the problem MIGHT be. Then go to main icon bar and click apply. Wait for it to finish. If it asks to remove orphaned dependencies try to refuse this (since you're going to add it back shortly) I tend to be paranoid so I'd restart before the next step. Next step is to take your list, search for them same way and add them back. ie mark for installation and then apply.
Even if this works the decoder reinstall leaves open the question of why it broke in the first place... If it doesn't work then ...?