You can "fix" this problem by not using chkdsk on active partitions. if you try an chkdsk on an active partition, windows will delay this operation until boot time, when it is unmounted and available to be checked AND any possible filesystem damage/corruption is fixed.
It is best to let chkdsk complete its job.
If you are seeing this stuff w/o running a chkdsk directly on an active partition, then I'd say your shutdown is failing properly leaving the disk in an unstable condition which can only be corrected by a chkdsk at startup time. Windows checks for this upon boot to you from mounting a damaged disk causing even more damage.