I have not spent a lot of time working withthe alternate layouts, so my knowledge is pretty sketchy, but my guess would be that you cannot split a TOC by layout unless you use different style names in the two layouts.
The good news is that when you create an Alternate Layout in InDesign CS6, the default is to create a new Style Group with the same style names.
So if you created your two TOCs after you made the alternate layouts, it might work. Haven't heard anyone doing it yet.
Try downloading the InDesign CS6 trial.
Thanks for both replies.
I'll download the trial version and give it a try. I just wondered though, usually when I export the chapter files in the books panel I select the required files and then export to pdf. If I have two alternate layouts in one of the chapter files, how would I specify that I want the print version (as opposed to the web version) of the two layouts to export with the rest of the files in the book?