Sorry I didn't post here again because I coudn't find older kernels where this 
didn't happen. I poked a bit in acpi and tried with acpi-call and found out 
that it is really the ec that gets confused and stops to report values. The ec 
could be reinitialized by adding or removing the kernel module msi_laptop 
(which will not load by default).
Since I do not use this notebook on battery very often I gave up on this.
But recently I saw that we have newer kernels in the repository. 
The notebook is still on precise and the recent 3.2.0-67 kernel still has this 
problem but I installed 3.13 linux-generic-lts-trusty some weeks ago and it's 
fine now.
So this was really a kernel bug that confused the embedded controller and its 
gone now.

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https://bugs.launchpad.net/bugs/889942

Title:
  ACPI power_supply battery errors to: No such device

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