I very seriously doubt it has anything to do with the operating system. As a matter of fact, I am 99% certain of it. And you really should have taken a look at the configuration before posting a question here.
What you are witnessing is probably some difference in the default key settings between releases of Eclipse on different operating systems, and/or between different versions of Eclipse. (Quite often, when you switch OS, you switch Eclipse version, too.)
It might be worth trying to export your settings from eclipse on windows, moving the exported settings file to ubuntu, and importing it into eclipse there. If that does not work, then you will need to fix the settings by hand.
You can configure just about any action in Eclipse to be triggered by just about any key combination.