Difference in how rye is used?

I think any grain, whether barley, corn, oats, etc, will have minor flavor differences depending on the water, soil, etc. Just like with the sweet corn that you buy at the store that has different varieties that also have minor different flavors, rye is probably the same. But I don't think that is the source of your different tasting experiences.

I suspect that because your experience with rye as a grain added to a 'rye beer' (it likely was not 100% rye, but was probably around 50-50 rye and barley (along with other minor grains that define that beer as a rye pale ale or rye amber style) or added to the stout that you mention, the incidents were early in your rye tasting career so that the different flavor that you experienced was new and unusual, so that your reaction was a dislike. That overall flavor may have been off-putting to you because it caused the stout to have a muted difference in taste (the rye flavor was fighting the roasted barley flavor that is what mostly defines a traditional stout) so that this minor change produced a negative opinion. (It's like eating chocolate on your spaghetti and disliking it. Chocolate is good, and spaghetti is good, but they aren't very good together unless you're acquired the taste for that combination.)

But when you had the rye in an IPA, that rye flavor was able to shine because the true rye flavor was more detectable due to the lighter malt flavor used in an IPA, or maybe because the 'peppery' flavor of the rye complimented the extra hops (or the specific hops) that are in that IPA. Also, your taste buds probably had become somewhat accustomed to accepting a rye flavor from your first experiences so that the next time that you try a 'rye beer' (whatever its recipe style might be), you likely will have a different opinion. Your taste buds will mature with your beer-drinking experience.