For reference, I have used "start /WAIT /AFFINITY 001 RustDedicated.exe -batchmode ^" as the initial (minus the :start and autoupdate stuff) line in my batchfile.
With "/wait /affinity" the console looks like this: Line 1Line 2Line 3"
Without it looks normal:
Line 1
Line 2
Line 3

> So my question is, how do i get my console looking like 'without affinity' but with affinity?

If ive messed something up this is the start/end of the batfile minus all the +server et al commands
@echo off
cls
:start
echo Starting server...

C:\SteamCMD\steamcmd.exe +login anonymous +force_install_dir C:\steamcmd\installs\server +app_update 258550 +quit
start /WAIT /AFFINITY 001 RustDedicated.exe -batchmode ^
//The +commands ^//

echo.
echo Restarting server...
echo.
goto start

legacy mode for the cmd console.. honestly who would have thought of that.