What adhesive are you using?
Perhaps the adhesive you are using is attacking the acrylic. When I replaced the leaking windows on my 89 H23 last year, one had been replaced before and the other was original. The previously replaced window had many small cracks and was noticeably melted where the sealant was applied (I don't know what it was.) The adhesive on the original window was amazingly pliable and the acrylic surface was not damaged. I called Hunter to find out what they used. Hunter advised it's Dow 739, an industrial Plastic Sealant/Adhesive. They said it was hard to find but I could buy it from them. I also found an alternate source at Neely Industries.