Peter,
Sorry that you are seeing this issue.
Can you give us some more details to help investigate the issue ?
1. Are the imported projects purely maven projects or created from an earlier release of MyEclipse ?
2. If they are purely Maven projects, then with which release of Maven are they created?
3. What are the target directories specified as ? Is there any specific reason why you do not want the target directories as output directories ?
4. How are you importing the projects ? Please give us steps in detail to help us replicate the issue.
5. What is the exact error you see when deploying to Tomcat ? Also mention the version of Tomcat.
6. Clear the contents of the .log file which is located at <workspace dir>/.metadata/.log. Replicate the issue and check the .log file for any errors of interest. If there are any, then please attach the .log file for us. Here is an FAQ on how to upload files to forums :
https://www.genuitec.com/forums/topic/troubleshooting-how-to-upload-attachments-on-forum/