This question can be asked in a variety of different ways, more notably: "My application server is failing to load my deployments because it tries to before the deployment is done".
The real issue is that the application server's "polling" time is set to such a short interval, that it's checking the new deployment directory so often and so quickly that it's trying to load your deployment before MyEclipse is done copying it out.
The only workaround for this issue is to increase your application server's polling time to a longer interval so it isn't checking so frequently.
One of our power-users gkelley
passed along the following information on the topic:
Even if an autodeployment fails, JBoss seems to continue to attempt to autodeploy the archive in the future. So, once the creation of the archive is complete, JBoss will eventually try to autodeploy it again. One can also customize the the "polling" interval for JBoss. For more info, see http://wiki.jboss.org/wiki/Wiki.jsp?page=ConfiguringTheDeploymentScannerInConfjbossSystem.xml