A few months ago I ran into an issue where after deploying ColdFusion to WAS 5 we could not get it deployed to a second instance running on the server. The feedback the WAS admin gave and the logs was very unhelpful. It turns out that if you create a second instance throught he admin console you can only use it for clustering. If you want to create a second instance that will be used for a seperate deploy you need to follow a different procedure. The procedure is outlined in a technote on the macromedia.com website. Thanks to Sarge and John Z for working this issue out.
BTW, these instructions work the same for any J2EE application you deploy on WAS including Flex.
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