I've started a new production, so new machine, new pipeline, new linux. So now I'm working with Maya 2010 x64, and Fedora 11.
After a day of fight, I've found that if you enable the option "Disable Evaluation" in the fluid shape after the cache is done, and you render the sequence in Mr, the render is always the same frame. If you render many single frames inside Maya render view all works.
The issue disappear after you disable that option (leave in practise as default), and the render go fine.
Is it only a my problem here? I don't think that there was this problem in Maya 2009... and in theory that option should disable only the calculation of the fluid, not the evaluation of the cache during the render.