jamiejackson,
Can you please answer some questions for me to investigate further ?
1) Can you share your build id from Help > About MyEclipse Enterprise Workbench? Please paste the build id here.
2) How did you install MyEclipse ? Is it through Pulse/All-In-One installer/Archived Update site?
3) Is your project a web project or a normal java project? Did you import it or create a new project?
I would recommend you a quick fix using pulse. Please do the following –
1. Open Pulse. (Start > Programs > Pulse > Pulse Explorer or download the same from http://www.poweredbypulse.com)
2. Start Pulse
3. Select appropriate Eclipse realm from the dropdown list. If you are on ME 8.6, select Eclipse Galileo; in case you are on 9.0, select Eclipse – Helios
4. From My Profiles, Select your MyEclipse profile
5. Right click on the same and click on re-install and run
6. This will open a wizard which will guide you through the rest of the steps.
Once done start the IDE, switch to a new workspace and create a new web project.
Here is the tutorial for Struts :
http://www.myeclipseide.com/documentation/quickstarts/struts/
You can also find lots of support material to get working with ME :
http://myeclipseide.com/module-htmlpages-display-pid-7.html
Let me know how it helps you.