According to "Hands On Agronomy" (book about Albrecht-style soil science), gypsum is to be used with caution because of its sulfur content. Apparently it is very important to use it in some specific cases, but in general I believe he recommends using a different form of calcium (calcitic limestone):
"Gypsum is a source of calcium, but it
should only be used when there is a need for calcium and the calcium saturation is above 60% in that soil."
According to the Albrecht system, Ca and Mg together should total up to about 70-80% of the total cation exchange capacity for the soil, so if you're already at 60% calcium it's pretty uncommon to need more of it I think.
I think the issue is that adding sulfur to a soil that doesn't need it binds up other minerals, but I'm not 100% sure I understood it right. Anyway, it looks like it's not a case of gypsum being "bad", just being called for in specific circumstances. I don't really have first hand
experience with it though, so I'm just parroting what I read from a book here...