Does Rashi's commentary on a quoted mishna reflect the true explanation?

Often the Bavli will quote a mishna from another maseches (tractate) or another part of the same maseches. Does Rashi's commentary on the Bavli's quotation of the mishna reflect his interpretation of the mishna per se, or does it reflect only his interpretation of the mishna as used in the Bavli? In other words, where there is ambiguity in a mishna, multiple ways to read it, does what Rashi writes when the mishna is quoted somewhere reflect only his belief as to how the Bavli reads it (and so any inconsistency is only a problem if it carries through to the Bavli's conclusion), or does it reflect his belief as to what the mishna itself means (and so should be consistent every time the mishna is quoted)?

I strongly suspect the former is true: in particular, I seem to recall having seen instances where a mishna is interpreted by Rashi in a way that satisfies only the initial theory ("hava amina") of a passage in the Bavli. But I can't think of any example of this, and would like some evidence one way or the other.