There have been many threads on the issue of "downgrading", all of which boil down to the issue that Minion has absolutely no way to tell which version is "newest". It can only tell you if a version is different from another.
Take tomQuest, for example. Here's the last several revisions:
r183
3.2 pre-beta2
3.2 beta2
3.2 beta3
3.2 beta4
(and so on until)
3.2 beta 11 (note space)
3.2 beta 12
(and so on until)
3.2 beta 23
3.2 beta 25
r244
These were all released by the author as "normal" releases.. some were technically beta, but weren't posted in the "optional files" area, and at some point you needed one of the betas because r183 didn't work well with some of the UI changes.
So how can Minion know that:
r184 is before 3.2 beta2?
3.2 beta2 is before 3.2 beta 11?
3.2 beta 25 is before r244?
It... can't. The best it can do is start comparing upload dates, but even that isn't infallible if versions are uploaded to curse on different days than they are on WoWI.
So the responsibility then falls to the user - figure out which of your addons are more frequently updated on Curse, and set Minion to ignore them. Do the same in the Curse client for WowI stuff. Then run both happily.
(Or do what I do: find a WoWI replacement for all your Curse stuff
The only thing I'm running that isn't updated on WoWI now is Recount.)