Is it possible that you have an over-aggressive virus scanner that is changing the modification date on the files? The hot deployer compares modification date from the last time it looked at the file with the current modification date to determine if the file has been updated.
Is it possible that you have an over-aggressive virus scanner
that's for sure not the case. Too bad.
Something is probably touching your files in /deploy. To verify this record the initial timestamps, and after a redeployment check again to see if something changed.