Comment 10 for bug 221651

I have the same issue, I can disable the "Legacy Fullscreen" and it works correctly, or if you dont want to do that, I found another workaround.
Change the command line to blender -w -p 0 0 800 600
This will force the window size to 800x600 (or change to whatever size you want) but you will have full window borders on it, so just maximize it after it opens.
I am also suffering from this bug: https://bugs.launchpad.net/ubuntu/+source/blender/+bug/571216
I dont know if it is related.