Magento + modman = 503 network error in checkout onepage

I have a problem installing modman on our Enterprise Magento store. We have two servers one on Linux and one on Windows (we have them like that for testing purposes). I am having problem with the server running on windows. The problem is that when I am trying to buy something from the magento shop running on Windows sometimes I am getting a 503 network error and in the error logs is saying that "Module "XXX" requires module "YYY"." I checked if the modules are there and they are I made all the files to be readable and writable - so the problem is not about rights. Also its not always the same modules missing, they are changing, but are from the one that I transformed with modman. I have a problem installing modman on our Enter