Well, if the .bat file is flashing, it's a different error, but I guess yeah. Since that Steam bug, it might not work to use the .bat file anyway.
If that's the case, you must copy some of the content of that .bat file into your Steam launch options. The .bat file will contain something similar to
Launcher.exe modname/config/main_init.cfg
You must copy that line EXCEPT the Launcher.exe part. Paste that text into the launch options by right clicking Amnesia in Steam > Properties > Set Launch Options.