Thank you for the replies @javiwhite and @pcjunki !
At the end of the day I found out the problem. Turned out AutoIT was looking for PsExec.exe in 64-bit format.
In another post I found a solution:
DllCall("kernel32.dll", "int", "Wow64DisableWow64FsRedirection", "int", 1) ;Prevent autoIT to look for 64-bit psexec.exe
After I added this line before where i call the batch file, everything works fine.
Anyway thanks for the replies guys!