I don't think I've ever seen an adequate explanation for this. Memory Alpha says the uniform tunic didn't fit him to start with so they were forced to put his comm badge up on the gray portion of the uniform for a few episodes, but I can't see why the uniform not fitting him would dictate where the comm badge goes. I mean, Riker wasn't forced to wear his comm badge in a different spot when he wore Sisko's hand-me-downs in "Generations".
Totally different uniforms.
Sisko's uniform in "Rapture" was a three-piece affair with a vest and jacket. The jacket was somewhat bulky and the greyish-purple shoulder yoke was a lot bigger and extended further down than everyone else's. To keep the combadge still over his heart, it was positioned there, rather than on the lower black part.
How is it that the comm badges were fastened to the costumes anyway?
Velcro. But when a scene required a combadge to be moved, sometimes a magnet was used.