Use copy-mode -q to leave copy mode

doc/vimux.txt

@@ -332,12 +332,17 @@ Default: 1
                                              *VimuxConfiguration_reset_sequence*
 4.4 g:VimuxResetSequence~
 
-The keys sent to the runner pane before running a command. By default it sends
-`q` to make sure the pane is not in scroll-mode and `C-u` to clear the line.
+The keys sent to the runner pane before running a command.
+
+When vimux runs a tmux command, it first makes sure that the runner is not in
+copy mode by running `copy-mode -q` on the runner. This sequence is then sent
+to make sure that the runner is ready to receive input.
+
+The default sends `C-u` to clear the line.
 >
   let g:VimuxResetSequence = ""
 <
-Default: "q C-u"
+Default: "C-u"
 
 ------------------------------------------------------------------------------
                                                              *VimuxPromptString*

plugin/vimux.vim

@@ -9,7 +9,7 @@ let g:VimuxHeight        = get(g:, 'VimuxHeight',        '20%')
 let g:VimuxOpenExtraArgs = get(g:, 'VimuxOpenExtraArgs', '')
 let g:VimuxOrientation   = get(g:, 'VimuxOrientation',   'v')
 let g:VimuxPromptString  = get(g:, 'VimuxPromptString',  'Command? ')
-let g:VimuxResetSequence = get(g:, 'VimuxResetSequence', 'q C-u')
+let g:VimuxResetSequence = get(g:, 'VimuxResetSequence', 'C-u')
 let g:VimuxRunnerName    = get(g:, 'VimuxRunnerName',    '')
 let g:VimuxRunnerType    = get(g:, 'VimuxRunnerType',    'pane')
 let g:VimuxRunnerQuery   = get(g:, 'VimuxRunnerQuery',   {})
@@ -73,6 +73,7 @@ function! VimuxRunCommand(command, ...) abort
   endif
   let resetSequence = VimuxOption('VimuxResetSequence')
   let g:VimuxLastCommand = a:command
+  call VimuxTmux('copy-mode -q -t '.g:VimuxRunnerIndex)
   call VimuxSendKeys(resetSequence)
   call VimuxSendText(a:command)
   if l:autoreturn ==# 1