I have both the trailing whitespace removal and the template enabled. It definitely removes the trailing whitespace from all other lines (I tested by adding some whitespace to a random line and watched the save action remove it). It appears to be an issue with the Javadoc configuration in the template itself. If you go to the Formatter in Eclipse (the template) and click on the Comments tab and enable the invisible characters, you will see the space before the CRLF in the template. I tried re-importing all of the IDE configs, just to make sure I didn't have older ones/out of date ones, but that did not solve the issue. The auto-formatting in the save actions appears to apply the template AFTER removing the whitespace, so it gets added back as part of the template (I am using Helios, btw). I am going to mess around with this some more just to make sure it is not something dumb on my end.