On my Fastmail account I see some message threads from my other IMAP folders also in my archive folder. This does not apply to all messages but only to those which are displayed as conversation threads.
Unlike Gmail and its “archive” label the Fastmail archive is not the union of all the other folders. If a message is in archive it is not displayed anywhere else.
The Fastmail webinterface and mail clients on other platforms do not show theses threaded messages in my archive, so this seems to be a displaying issue only present in eM Client.
I am using eM Client 7 RC on Windows 10 Pro 64 Bit. Please ask if you need additional information to reproduce this issue.