Ok, I've heard multiple complaints about ArcadeOS saving over settings - I can suggest a quick 'n dirty fix
first, copy the correctly edited arcadeos.cfg to a new directory, such as C:\BAK
Next, add the following line to autoexec.bat
COPY C:\BAK\ARCADEOS.CFG C:\ARCADEOS /Y
(The /Y denotes auto-overwrite, makes life simpler)
Bam! Everytime you restart the machine, you have the correct config file. Cheap, dirty, easy. Just the way I like 'em