I'm not 100% clear what you're trying to do - "the output statistic files separate each ROI and all of the data consecutively" doesn't make a lot of sense to me, but there's the "output ROI to ASCII" option - is that what you're saying doesn't do what you want? If it doesn't, it'd be pretty easy to write a little code to make ENVI output whatever you want. That text format you mentioned with ROI's as rows and stats as columns would definitely be possible (and likely pretty easy), for example...
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