That should not be happening and I have no idea how to reproduce the behavior. It’s not happening on the one from from stretch-testing, and it appears you have identical settings. I’m going through my about:config and nothing else should have that effect. I don’t know for sure what to do here, I could help you use the new one and configure apt to only update the required packages from stretch-testing. I’m sure that would solve the issue. But it would require mixing stable and testing repos which is usually a no-no. Or I could give you a user.js file to download and a command to run, as long as you know the path to the directory where you have your Tor Browser Bundle installed. If it’s installed by Whonix, the path is likely $HOME/.tb/ which I can also work with.
Personally I don’t think i2p-over-Tor is necessary(and it tends to make things quite difficult) but I’ll do my best to help. Should you decide to forgo i2p-over-tor, then https://github.com/mutedstorm/Whonix-I2P is the most current set of instructions.
I’ve got to run out for a moment, I’ll be back shortly.
Edit: So sorry, those instructions for i2p-over-tor don’t look like they’ll actually work for i2p. i2p-over-tor is possible, but ws-tor-i2p-web as described for the other types of proxies here is not how you do it. The analogous thing to that would be using an i2p inproxy in regular Tor Browser, not modified for i2p. i2p can also have some of it’s low-level traffic proxied, and it’s possible to do that over Tor, which is why I was confused.