Are you using the latest connector version 1.4.0?
Can you please tell me the exact steps on how to reproduce this?
I remeber i was able to reproduce it, but now i can't.
Guess I don't have notifications here, sorry for the late reply.
I just updated to connector 1.4 (not sure what I was on before), and same thing still happens to me.
These steps should work
Start exporting any clip in Premiere to open Export Settings (I typically press CTRL+M). Pick format Voukoder - click Configure under Voukoder settings and choose VP9/webm output, click OK. Click Save Preset and give it a name (you probably don't even have to do this) - then export your clip. This part will work normally.
After it's exported, try to export the same or any other clip again - it should default to your saved webm preset but the output name changes to mp4. You can then click Configure under Voukoder again, and it says the codec is still VP9 - press OK, and it changes the names back to .webm
I have found that if you actually export it without changing this, it will still export as intended the webm. However, it will not warn you if a file already exists with the name and will automatically overwrite it. Even if you try to change the file name, the browser only looks for .mp4 files so if you have webm's already created, you won't see them there to make sure you pick an unused filename.
I also tested changing to other formats and it doesn't seem to make a difference. Even if I do h264/h265/vp8, if I pick any output format that isn't mp4, it will always change the filename to mp4 when I try to export a second time.