The problem is that TradeJunkie's existence will cause Minion to write it to the configuration file (ignored or not). The configuration file stores all of the information regarding what version Minion believes you have installed. This data becomes invalid when writing TradeJunkie's data, so Minion throws it out to try to recover. Since it's thrown out every time, Minion has no way of knowing the current version of any of the other addons (not just TradeJunkie).
The only way I can think of stopping this from happening is removing TradeJunkie from your interface folder. This isn't a very acceptable option, though
