I haven't experienced this specific issue myself, but it could be related to the migration process or maybe some settings got tweaked during the upgrade.
Just wanted add that I fixed the issue of passwords not accepted when logging in from connection-manager in addition to old fix posted here about tray passwords not working, and updated links(all of them, deluge.exe rebuilt etc, except the ticket) a few posts above. Also, the former fix for tray passwords I noticed only worked for return/enter presses and not actually pressing button doh, so that also works now.
I haven't decided if confident enough to post a PR with this little fix, or just add a ticket - it's still same issue of dialog destroyed before gtk.entry read finished, and I added async delay to destroy function of inherented base-dialog, to catch both these issues, actually no delay needed, as just wrapped in async callLater with delay 0 enough, but as said, not sure if they would do it in another better way, but i'll figure that out one of these days and edit in a link to ticket or PR here, just if wanting check activity on it later or something. Sorry for screw up before with only accepting return/enter for accepting password. Hmm, with the source open in another tile, I got another idea possibly, but regardless, above works, so will not change it and rebuild deluge.exe etc just for something end user cannot differentiate anyway, so as said will think little about it, but the fixes here fine for end-users atleast, and tested on linux and win10 VM.