If you are affected by this problem, please try installing http://repo.turris.cz/omnia-dev-ondrej/packages/turrispackages/knot-resolver_1.2.6-1_mvebu.ipk
Download the package to Turris Omnia and install using opkg. Something like:
cd /tmp
wget https://repo.turris.cz/omnia-dev-ondrej/packages/turrispackages/knot-resolver_1.2.6-1_mvebu.ipk
opkg install knot-resolver_1.2.6-1_mvebu.ipk
And please report back whether it has helped you or not (it should). The problem manifest itself only with slightly unreliable authoritative nameservers (or networks) that makes some packets to be lost.