[Galaxy Note II Accessories] Logicfail:
This happens because wacom digitizers use magnets to work (partially, there's more to it) - the pen is a magnet. Crash course: A magnet creates a magnetic field around it. Whenever you're moving the pen, you're moving this field - any given point in space near the magnet experiences a change in this magnetic field (this creates an electric potential and a potential difference between points affected by the field). A really cool thing about moving magnets near wires is we create what's called an induced EMF - the change in magnetic fields causes electrons to move because of changes in relative potential difference between nearby points.

A static magnet (in relation to a point) will have a static field, but a field none the less - the magnet on the casing. When you bring two magnetic fields together, they interact to form a resultant field at any point in time.

The pen is still working as intended, but the other magnet has changed the potential you produce near that magnet via movements of the pen - thus, different and incorrect readings. It's relative to the position of the case magnet, so you get a different effect at different distances from the magnetic source.

The result is that the same motions of the pen near that magnet are causing different currents to be read than the wacom digitizer expects for that motion.

While it's great to hear through some empirical data that physics still works, I was already actively avoiding this case for this reason.

In contrast, previous smartphone cases with phones that use capacitive touch don't have as much an issue because it's basically a field of current that your touch (finger, capacitive stylus, etc) redirects some of that flow across. While a magnet could indeed affect this field, the magnet isn't moving so it's not as much an issue (it's still an issue because, depending on field strength, orientation, and relative locations, the electrons are still moving with respect to the magnet, and are repelled/attracted by the field in this manner to different degrees. However, the difference is constant and like is accounted for because digitizer system can't guarantee constant currents necessarily, so there is variation allowed for. With the Wacom pen magnet, it's weak enough to be noticeable.

TL;DR - Anyone with a course in EMF and an understanding of induction would be able to tell you this right off once they found out the pen uses a magnet. Incidentally, the magnet is also why you can do the hovering stuff so accurately. Other forms of non-touch gestures have many ways they could work too, but one way is your body affecting a field around the digitizer enough (whole hand swipe across without touching) that is is measurable.

It's also how inductive chargers (ones where you don't plug in the device) work. Changes in current flowing through wires creates a magnetic filed which, by orientating the wires, using loop/solenoid type configurations, this field changes (an AC signal). When your device is in the field, a similar configuration in the device is subjected to this changing field, and, more simply put, energy is exchanged via magnetic fields.

This is really cool because you've taken a changing current, which creates an electromagnetic field across other wires, which causes a flow of current.

Anyways, yeah avoid having magnets near devices depending upon EMF induction to work :P