montana01,
Sorry that you are running into this issue with MyEclipse.
Can you answer some more questions for us to be able to investigate the issue?
1) Which server are you deploying your application to? If you are working on WAS then please provide us details about server version Execute {WAS location}/bin/versionInfo.bat script from the console and copy your output details here.
2) You need to start the server in Debug mode for changes to Java classes to be picked up. Are you doing this? Also, if you make a change to a JSP file directly (like a simple text change) are those changes showing up?
3) What kind of a project is it ? Is it a simple Web project or an EAR project ?
4) Make sure that the ‘Build Automatically’ is checked on.
5) Could you paste here deployment log? It is located under directory .myeclipse/logs in EAR project. Before sending, please delete that file, perform deployment and hot-syncing.