Not clear whether you're saying this is happening to all channels or that you just join the 1 channel.
Options/display/options - Windows
... has a list of things that open as a desktop window, and a checkmark in there would cause all channels to open on the desktop
Also, if you use /help /join
... and choose the 2nd item, it shows the syntax for /join has an optional -d switch for making that be a desktop window
/join -d #OpenedOnDesktop