I think this has to do with an annoying feature of Windows – I’ve had something similar for a long time in different programs (not just Eclipse).
If you have a non-English version of Windows, you probably have different keyboard layouts installed (for example, I have a Dutch and a US English layout installed by default). The key combination Alt + Shift switches between keyboard layouts. It’s very annoying and it’s a really strange feature – as if the keys on someone’s keyboard would suddenly change?!
You can go into Control Panel, Keyboard Settings and remove the layouts that you don’t want to use. (I removed the Dutch layout so there’s only US English left), so that you can’t switch to the wrong layout by accident again. Or you can go to the Advanced Key Settings in Keyboard Setting and turn off the key combination.