think this may work, i had a similar problem, in Eclipse
try any one of the below set of steps.
1.every time you make changes,
2.build and clean your project,
3.and you can right-click on your server and the click clean. (the IDE will remove all the old files and then deploy your new deployment. )
you can also use this method,
1. After making your changes you can clean your project.
2.right click on the server in servers window, then click on Explore, this will open folder where the deployments are present, then you can delete the deployment manually.( ie this folder will have the war or the Exploded form of war, you can select the war and delete the war by simply right click and delete)
3. now right click on your project and run on server.
the reason behind this problem might be due to the fact that, the deployment is done once and the next time the IDE does not properly update the deployment,
there is also on more possiblity, that your project might be large, that might also affect the refreshing time, or your system might be running so many othere process so try to remove the unwanted process from your
task Manager,
(ie open your task Manager and then select process tab and then select the process that are not useful for you, thus the system performance will increase).
these are possible answers that i can give you, so try them.