To resolve an issue with DNS you can change all your filters from blocking to redirect and check filter ID in the DNS packets. So you can identify filter which selects DNS packets.
What is the “filter ID” and where is it to be found?
There is a variable called m_FilterID in structure INTERMEDIATE_BUFFER, but only in WinPkFilter 3.1.2 (and possibly later versions).
I had been using WinPkFilter 3.1.1, and it did not have such a variable.