You are doing CHKDSK on a live system. CHKDSK only reads the data structures on the disk, not the log and not what may be cached in RAM. This is almost always going to return discrepancies and is totally expected.
In your case, above, a file may be created. NTFS puts all this information into the log but doesn't necessarily write out the directory or the file record (they are written in RAM, but haven't made it out to disk yet). If the directory is written out and not the file record, CHKDSK will see an invalid directory entry (the file record is inconsistent) and then report that the directory entry needs to be deleted.
Dismounting the volume, flushing it, or shutting down will cause all the cached data to be written out which will return the volume to consistency, hence CHKDSK on boot reporting no errors.
Lastly, if you crash, since the log has been written out, upon restart NTFS will read the log and update all the disk structures to bing them back into consistency. Standard database stuff.