.properties files sometimes omitted when deploying a webapp project to Tomcat

I have a manually created web project with the standard maven structure (src/main/webapp, src/main/resources etc.). When I deploy the application to the server using Eclipse (Servers view > Tomcat 5.5.27 > Add or Remove Projects... or Publish...) it happens sometimes that .properties files (such as log4j.properties) from src/main/resources are not copied to the server.

For some time everything worked correctly but then this problem appeared and I cannot get rid of it. A friend had the same issue and solved it by not using the m2eclipse plugin (he only used a maven goal to generate an Eclipse project from the maven project). This would suggest that m2eclipse is the guilty one but on the other hand it could also be some random corruption in project/Eclipse workspace.

I don't know whether this is actually m2eclipse's or Eclipse's issue and would appreciate advice how to find out more about the cause.

The strange thing is that this worked and now doesn't. Removing and Adding the webapp to the project doesn't help, neither dies cleaning its tmp folder. The WST config file .settings/org.eclipse.wst.common.component looks all right.