I had the same problem with my "issue gortex cold/wet weather boots", they would squeak non stop, even after my 3rd year of breaking in? So this wknd with my B-Day money I bought me a pair of "Muck Hunter Boots" there good till -27c, they're light, waterproof and comfy!!
I used Dubbin on my 1st Gen issue Gortex and it worked great, the only problem with those boots were they don't breath, I still wear them in the early fall and around the yard. Anything to soften the leather seams wise, to rid the squeak, I did'nt apply any of this to my cold/wet weather boots cause I don't want to have to pay for them.