[Shirik]

Minion attempts to resolve conflicts by using whichever module claims a higher version number. Sometimes, however, this isn't exactly "correct" (for example, when one site might use an SVN revision number and another site might use the actual version number). In this situation, you can manually override it via the mechanism Cairenn already suggested -- ignoring an addon is per module, so you can ignore it on one site and not the other.