System: Vista64 SP1 on one harddrive, XP SP3 32bit on another harddrive. I swap drive priority in BIOS to dualboot, Vista IS hidden from XP (to preserve Restore Points). 4GB of memory is MemTest+ 2.01 stable, memory is Prime95 stable (don't even think that the memory is a problem). CPU is e6600 at 3.2GHz, also stable and not overheating.



Every time I run Vista64 then shut it down to reboot into XP, chkdsk runs. Chkdsk never (really... never) finds any problem. Oddly, the only partitions it checks is the XP (now "C:") and another data only partition (H: ). The H: partition was never deliberately accessed (or modified) by Vista although anything could have been done by the system without my knowledge. All partitions except the Vista C: partition have had indexing turned off (in properties), I have not turned off the Vista Indexing service (yet). When the XP chkdsk runs (the DOS version running at boottime) it does not check the partition that Vista is on, only the XP partition which is on a different harddrive than the Vista partition. If I reboot into Vista no chkdisk is run.

Why is chkdisk running when Vista has seemingly had no trouble while running?

The BootExecute variable is already set to the "don't always run at startup = autochk *" setting is both Vista64 and XP. I don't think that's the problem.

To clarify:
No chkdsk runs if I boot Vista after shutting down Vista.
No chkdsk runs if I boot Vista after shutting down XP.
No chkdsk runs if I boot XP after shutting down XP.
Chkdsk runs if I boot XP after shutting down Vista.