The easiest interpretation would be that as for Adepts if you have a power active you suffer a penalty to all you actions, magical or not.
That seems to be an okay rule of thumb. However, I want to play it by the book, or rather, as intended by the writers.
The missions FAQ says "skill tests" augmented by magic. That is a lot clearer than the SG description, but
- For one, there's still some ambiguity. For example, Critical strike. It doesn't affect any tests, it's just raising the DV. You don't roll any dice with DV, it isn't a skill test, it's being added to the result of a skill test. Would the attack test be still affected? Based on the FAQ, I think not, but still, it's linked to a skill, so?
-For two, I'm not sure there isn't any official source overriding the Missions FAQ, or that is it the most recent and official ruling?