We use Contribute with sites set up for check-in and check-out with DW. We
update and intermediate server which executes a script to update production
every few minutes.

When we update our site with either DW or Contribute the file to be edited is
deleted immediately, then replaced several minutes later when the "staging"
server updates production via the script.

Is this related to Check-In being enabled, perhaps or is anything else that
you know of causing it?