Eugene,
I could not replicate the issue at my end. If I Ctrl+Save while debugging, the debugging process shifts to the first line of that function and restarts debugging from the beginning of the function. I checked on Tomcat 7.x and JBoss 7.1.1.
Please switch to a new workspace and check if you see the issue with a sample project. If you are working with a different server, please share the details. If possible, please also check if you can replicate the issue with Tomcat 7.x.
If you have installed any third party plugins, please list them.
Let us know how it works for you.