Maybe it’s just me but noticing some disparity with how PopClip appears when selecting text via clicking it, vs when using AppleScript to trigger it to appear.
If the method you are using is stealing focus from the current app then PopClip will be showing its bar according to the newly focused app not the one where you selected the text.
Had this come up recently with a user who was triggering it via BTT url scheme into Alfred. Alfred was activating and stealing the focus.