I can only speak based on my experience of generic WinPE, but as you probably know, the WinPE boot process basically mounts the boot.wim file from your boot device (USB in your case), and by default the RAM based WinPE image is booted to the X: drive
During the WinPE boot, a file called startnet.cmd is executed, which starts wpeinit.exe - and this file is in the x:\windows\system32 folder, which is part of the content of boot.wim.
Normally, if generating a WinPE utility disk for general support work, I would add a line to startnet.cmd, which will locate the drive letter that the USB device is on, and then run my "go.bat" file from there, as this allows me to edit go.bat without having to mount boot.wim, edit it, and then unmount it.
If your start.bat file is external to the WIM file that your USB device boots from, then I would guess that your wim file has additional content in its startnet.cmd file which is taking precedence over whatever is in your start.bat file.
I don't have access to a GSS-created WinPE boot system, as I use my own WinPE system with an old version of Ghost32.exe to provide a portable boot and recovery environment.