Not saying this is related to your issue but I am wondering from if you add something to harden the water? It sounds like you use spring water for everything. As far as I know (from reading), brown ale and rye ale wants hard water. By the way you can break down chloramine from boiling water in 20 minutes. I know there are additives to harden water but I plan on using filtered city water for my beer (if filtered water is good enough for my cooking, etc, why shouldn't it be good enough for my drink? 
I'm interested in this problem though. And I find your 1 gallon batches interesting. It allows you to try various recipes very quickly doesn't it?
I'm interested in this problem though. And I find your 1 gallon batches interesting. It allows you to try various recipes very quickly doesn't it?