Same issue here after upgrade to 16.10.
Here is the log after connecting to VPN:
Switching to system DNS server 10.1.96.48.
Cache miss for daisy.ubuntu.com IN A
Transaction 29603 for <daisy.ubuntu.com IN A> scope dns on */*.
Using feature level UDP+EDNS0+DO+LARGE for transaction 29603.
Using DNS server 10.1.96.48 for transaction 29603.
Sending query packet with id 29603.
Timeout reached on transaction 29603.
Retrying transaction 29603.
Switching to system DNS server 10.1.96.49.
Cache miss for daisy.ubuntu.com IN A
Transaction 29603 for <daisy.ubuntu.com IN A> scope dns on */*.
Using feature level UDP+EDNS0+DO+LARGE for transaction 29603.
Using DNS server 10.1.96.49 for transaction 29603.
Sending query packet with id 29603.
Timeout reached on transaction 29603.
Retrying transaction 29603.
Switching to system DNS server 10.1.96.48.
Cache miss for daisy.ubuntu.com IN A
Transaction 29603 for <daisy.ubuntu.com IN A> scope dns on */*.
Using feature level UDP+EDNS0+DO+LARGE for transaction 29603.
Using DNS server 10.1.96.48 for transaction 29603.
Sending query packet with id 29603.
Later on:
Lost too many UDP packets, downgrading feature level...
Using degraded feature set (UDP+EDNS0+DO) for DNS server 10.1.96.48.
Using feature level UDP+EDNS0+DO for transaction 35344.
Sending query packet with id 35344.
Timeout reached on transaction 29603.
** Changed in: systemd (Ubuntu)
Status: Incomplete => Confirmed
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https://bugs.launchpad.net/bugs/1624317
Title:
systemd-resolved breaks VPN with split-horizon DNS
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