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Using Maya, sometimes you can experience issues when try to export a .mxs sequence with any sort of RealFlow meshes embeded. Looks like there's not a fix for that in the short term as there are some problems in the Maya side that scramble the code of specific plugins creating unexpected errors (you may experience this when both RealFlow and Maxwell Render plugins are set to Autoload in the Plugin Manager) and get some odd obscure results in your renders. If you try to export a .mxs and get just a .ma file istead your .mxs files, you can try this simple script (thanks to Next Limit's Angel Tena) to automatically enforce Maya do the job via MEL.
Don't forget to customize your own scene length, framepadding and file path for export the .mxs files