Is there a write cache enabled on the drive? It could be the data has not been written to the disk and running chkdsk flushes the cache making the file appear.
I am not too sure how NTFS or if NTFS uses a File Allocation Table (FAT) if it does it could be possible that this is also being cached. So an update to the FAT on one machine will not reach the disk until the cache (or buffer) is flushed.
This is a little far fetched as the caches should be periodically flushed anyway so we are only talking about a few seconds before the data is actually written to disk.
That said I would still investigate it.
I am a little confused about what you are trying to acheive though. One machine must be the "owner" of the drive. This is how network shares work and how multiple clients can connect to the same share without conflict.
What you are trying to setup is where both machines believe they own/control the disk. We have a number of RAID boxes here all with two SCSI interfaces for hosts so that we can cluster the boxes. When you cluster two machines you specify a that drives (resources) are owned by specific nodes. This allows the cluster service to co-ordinate writes/reads etc.
You are lacking this form of co-ordination. Neither box will be aware of the other and WILL conflict. For example, what if each box tries to create a file in the same location on disk at the same time? Who knows who will win. The result will be a mess of a file (if your lucky, unlucky = no more data).
You could probably get away with this kind of setup if one machine writes files and the other is just reading. In that case we must make sure no data is being cached at all and it is all written to disk straight away. Thiswill degrade performance somewhat.
I hope that helps.