Q: Is Chkdsk something to stop to enhance performace once XP or 2000 pro is running and stable? Or is this something that only runs at startup then once complete does not run til restart?
A: Chkdsk is a program which checks the integrity of a disk's file structure. The MS-DOS / Windows 9x version does not check the physical condition of the disk, but the Windows 2000 / XP version does (if the /R option is specified).
When Windoze boots up, a "dirty flag" is set for each disk in the system (if anything is written to the corresponding disk cache). When Windoze shuts down properly, the "dirty flags" should be cleared. If Windoze crashes or doesn't complete shutdown properly, the "dirty flags" may remain set. This may or may not indicate a disk integrity problem.
When Windoze next boots up, chkdsk is run to check (and repair) the file integrity of any disk for which the "dirty flag" is still set.
Thus, Chkdsk is only run upon system startup (and then only if Windoze thinks it wasn't shut down properly last time). It can also be run on demand while windoze is running (if you have reason to suspect the integrity of a disk), but it won't do so unless manually initiated.