VL, I think you are on the right track with it being the windows. On my 3000 gal. build I used PA and dow 832 with acrylic windows. Its like Deja Vu all over again; I experienced the same thing you have. multiple coats of PA, still leaks, doubts, frustration, etc. Its not your construction, its not flexing, its not pin holes, its not the water depth, its not the Pond Armor! Its that acrylic doesnt seal well with the silicone sealant. Period. If you decide to take out the windows to try to reseal, Dow makes a primer to use for difficult surfaces; (Dow Corning PR-1200, RTV Prime Coat) you could try that. I did not use it, and my tank still has slow intermittent leaks after almost 3 years in operation, but my tank is outside so I dont care about the small leaks. When its time for a major recoating/maintenance, I will remove the windows and use the primer.
Good luck, and dont let the set backs get you down!
PS: A Dow rep. recommended the primer back when I was working on my tank, but I didnt listen. I was reluctant because it sounds like nasty stuff (strong fumes, etc.).