What prompt are you seeing in these cases? Do you see an elevation
prompt or the prompt asking if you want to import a registry script?
Are you trying to write to HKLM registry keys which are virtualized by
process bitness?
When you run the BAT from SlickRun, do you see any error messages in
the console?
I suspect the most likely explanation is that you're running the batch
file from Slickrun by pointing directly at the BAT and the result is
that a 32bit CMD prompt is spawned which then results in a 32bit
RegEdit instance, and you only end up writing to the 32-bit
virtualized versions of the registry keys. You could use SysInternals'
Process Monitor to verify if that's the case.