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This is an intermittent problem. Here are steps to reproduce, but it doesn't always reproduce Create the Depot sample app. Do a rake > rails update. Migrate the database. Right-click the project node and choose Properties. Make the server WEBrick and the port 3000. Run the project Go back to the properties and change the server to GlassFish and leave the port 3000 (I know this isn't correct but do it anyway). Run the project. It runs in the WEBrick server. Now change the server to 8080. It still runs in the WEBrick server. If you stop the WEBrick server it will then try to run it in GlassFish. I noticed this problem when I changed the server but forgot to change the port number. After fixing the port number to match the server, the IDE was still using the old port number. The work around is to stop the servers before rerunning (I think).
Yes, the workaround is to stop the server before rerunning. If a server instance is running for a project, the run action will use that automatically. Looks like it should check whether the server configuration has changed and if it has, stop the current server process and start a new one. I think is not a particularly common scenario though, and the workaround is straightforward, so I'm downgrading this to P4.