Please try switching servers using the Network option or the green dot button in the bottom-right. Try making the same payment from a different server.

The dust threshold depends on the min relay fee, which is a server setting. Thus, it is server dependent. At this point, this threshold is not sent by the Electrum server to the client, but it is a default value, hardcoded in the client. That default value might be lower than the value set by the server you are using. Try to use another server.