Ok, what does maya say when you run a render form commanline (no not from within maya form the operating sytems commandline.) Anyway you can render with per frame forcers but yoru giving most other uers a 20% advantage, so ist stupid as it probably eats all benefit of getting faster stuff in firstplace.
Se this is what happens. Maya comes in 3 flavours, GUI maya , batch maya and commandline render maya. Commandline render maya is a stripped down version of gui maya, because it does not need to know gui stuff, just render stuff. The commandline render maya is also free for you as long as you have one licence, so you could use a 100 computers for one licence of maya (this doe not extend to mentalray or hardware rendering tough wich use batch maya licences trough commandlin render maya).
Now whenever you call batch render maya saves out whatever you have to temporary file, it then passes this file to commandline render maya wich has absolutely no idea what your doing in your GUI, IT has no usnderstading of your gui. NOTHING NADA ZILCH.
This is why you need to make good care to understand, how the commandline operates because maya sdependent on you KNOWING this, also define your projects very well and make sure to chak that maya passes this info along aswell. Also maya batch need same rights as GUI maya wich may or may not be the case.