Issues with creating SOAP WAR

Creating the SOAP war file usually works the first time if it's a brand new file, but if I need to regenerate the file for whatever reason, I have to attempt it 3 to 4 times before it will actually work. I thought it was something filesystem related, so after each failed attempt, I would refresh my project tree using the double refresh arrows, or I would right-click on the parent node and click refresh. If I'm lucky, it'll work right after the refresh trick, but it usually takes 3-4 times of trying before it finally takes.

This was also happening on JBDS 9.