A little while back, I managed to successfully make legal shiny Raikou, Entei, and Suicune from Colosseum in Gen 6 for the purpose of getting all the ribbons on them going forward. I decided it would be fun to do this also with other Shadow Pokemon from Colosseum, namely those that gained new evolutions in subsequent generations, and I made a Sneasel that was perfectly legal and now is a Weavile in Violet with all possible ribbons. I went ahead with some others, but all of these for some reason showed the ORAS contest ribbons as illegitimate (this might be an issue with affection from what I've read in other threads, not positive about that though because after fixing the affection there wasn't any change). A few showed a PID nature mismatch even though I had double checked the natures and a couple even showed an encounter type mismatch which really shouldn't be the case considering there was only one way to even have the encounter to start with.
If it helps as additional context, what I've been using for this is the November 17, 2016 release of PKHeX- it's unfortunately the most recent version that I can get to play nice with Wine Stabl e on my Mac. At least some of this easily could be either the result of using such an old version of the program or just me making a dumb mistake, but I'm still extremely confused by it when the previous four Pokemon I made turned out perfectly fine with no legality issues.
I really appreciate any help with this in advance, it doesn't make sense to me what exactly went wrong with this.
153 ★ - Bayleef - DC5BAF3C102C.pk6
156 ★ - Quilava - DD5C30B09214.pk6
156 ★ - Quilava - DD5430B09214.pk6
159 ★ - Croconaw - F46243870CC4.pk6
176 ★ - Togetic - 85942378C044.pk6
190 ★ - Aipom - AA2243870CC4.pk6
193 ★ - Yanma - 67D0C27D2130.pk6
198 ★ - Murkrow - 637D9FE00AE8.pk6
200 ★ - Misdreavus - C9E330B09214.pk6
206 ★ - Dunsparce - BEDB9FE00AE8.pk6
207 ★ - Gligar - BB7BB833E4FC.pk6
212 ★ - ハッサム - 2957C66253A7.pk6
217 ★ - Ursaring - 1052B833E4FC.pk6
221 ★ - Piloswine - D4E243870CC4.pk6
234 ★ - Stantler - 11482378C044.pk6
248 ★ - Tyranitar - 8E899FE00AE8.pk6
376 ★ - Metagross - 2AB443870CC4.pk6