I get this too, mostly with magnet links.
But it seems to only be after browser updates for me - definitely not on every browser start.
Problem is I've been unable to reproduce this from a clean profile and without that I can't really report a bug as it can't be confirmed (even if as a Soprano tester I can confirm my own bugs...)
Technically, the preference is stored in the file Preferences in the profile like this:
"protocol_handler" : {
"allowed_origin_protocol_pairs" : {
"https://1234x.to" : {
"magnet" : true
},
"https://pathduck.github.io" : {
"ftp" : true,
"magnet" : true,
"sftp" : true,
"tel" : true
}
}
},
So apparently, something causes the protocol_handler preference to be reset, either on update or possibly in some cases on every browser start.
If someone can figure out what or how to reproduce this starting from a clean profile it would help a lot nail down this.
Some test cases here:
https://pathduck.github.io/test/links/