After installing the last update of Glassfish tools for Kepler I got some meanfull message which actually help me solve the problem and now I can run Glassfish in debug mode.
Here is my workaround:
Go to your .\glassfish4\glassfish\domains\domain1\config
folder.
Open domain.xml
file in any desired editor.
Navigate to ./domain/configs/config[name=server-config]/java-config
node.
You should have an attribute debug-options
as below:
debug-options="-Xdebug -Xrunjdwp:transport=dt_socket,address=9009,server=y,suspend=n"
Remove " -Xrun" and it should look like:
debug-options="-Xdebugjdwp:transport=dt_socket,address=9009,server=y,suspend=n"
Save. Restart/start Eclipse Kepler and should be able to run Glassfish in debug mode again, if you had similar problem like mine.
Hope this helps.