No, not ideal, by any means, and certainly annoying. But, on the
other hand, it doesn't sound especially serious, either, since you're
able to continue doing what you like until the next reboot.
No, you needn't purchase a new disk.
When you installed SP2, it should have created and left a folder
entitled "i386" somewhere on your hard drive. When the System File
Checker asks for the Windows CD, simply browse to the location of this
/i386 folder.
If, you some reason, there is no such folder, you can download
(perhaps using another machine if yours is too uncooperative) the full
copy of Service Pack 2 and use it, along with your original installation
CD, to create a new installation CD with SP2 built-in. This process is
known as "slip-streaming."
For slip-streaming the service pack and subsequent updates to WinXP:
How to integrate software updates into your Windows installation source
files
http://support.microsoft.com/default.aspx?scid=kb;en-us;828930
SlipStreaming WinXP
http://www.webtree.ca/windowsxp/slipstream.htm
Additionally, you should check your Event Logs to see if they can
shed any light on the matter. This could be particularly useful on the
off-chance that the "barking" messages aren't being caused by missing or
damaged Windows files. To do so, Right-click My Computer > Manage >
Event Viewer > System and Application. Record the specifics of any
red-flagged error messages and post the exact text back here. Hopefully,
one of us will be able to provide further insight.