Transparency Flattener only affects a few pages

I'm trying to use the transparency flattener to essentially rasterize all the text in a PDF. (Before the pitchforks come out, it's for legal reasons... hands are tied.)
I open the Transparency Flattener preview, move the Raster/Vector slider all the way to 0, change the dpi to 400, select the All Pages radio button, hit apply, and it seems like only a random sampling of pages actually gets rasterized. Most text is still selectable. Any ideas on how I might go about figuring out what's going on? I've done exporting each page to an image, then recombining to a PDF, but the file size is just too big.
Using Acrobat XI Pro on Windows 7.

Options:
- Open the files in Photoshop and save as an image PDF.
- Export all pages as TIFF/JPEG and then re-import them Acrobat.

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Transparency Flattener only affects a few pages

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