So I have a strange issue. When using Chromium on the Nexus 7 port of Ubuntu, Java apps in the browser have the cursor flipped, literally (not just inverted movement, but the cursor itself flipped too).
Also, clicking in java apps, both in the web browser and standalone, clicks don't register when using a USB mouse. I have to tap the screen itself to click.
And another issue with the mouse; it seems Minecraft is unable to run, and freezes with an error similar to being unable to "GetInput", possibly related to the clicking issue above.