Numbers wrong in minor key?

I appears that the generated numbering system is wrong when a minor key is assigned to a song. I checked a bunch of songs rooted in natural minor & the chord numbering (e.g., sharps, flats, etc.) appear to be drawn from the parallel major key (NOT the relative major key)

I may be confused, but songs in A minor with only diatonic chords should have no sharps or flats; however, the number system seems to assign flats to chords as if the song is written in the parallel A major key. I checked a bunch of songs & drafted my own to check this. It seems to be corrected if a song is assigned the relative major key....then the autogenerated #s follow a Nashville numbering system.

Please let me know if I'm trippin', but I don't think so (kind of a theory amateur, but not total newbie).

I'm not sure about the issue you're describing, but I do know that it can often times be more useful to create a chart listing the related Major key instead of minor, and that would likely fix what you're describing above.

Example: beginning chord progression for House of the Rising Sun in Am
Am C D F Am C E
In the key of Am, that'd be
1m 3 4 6 1m 3 5
If you list it in the related Major key of C-Major, the numbering would be:
6m 1 2 4 6m 1 3
Setting the song key to the related Major like that should solve the issue you're describing, and for most people it's a little more intuitive to read the numbers/chords that way as well. Hope that helps.
-Tim Gross

iRp chart examples
A- chart
A- number chart
C number chart