I have not been able to reproduce this. If you haven't solved it, it might be a good one for our support team. You can fill out a form at: http://www.tableausoftware.com/support/request
I would not expect the axis formatting to have any effect on the crosstab contents. You are probably picking up the data as it was fed into the viz from the raw data. If you change the Date Format of the date field(s) in Desktop, to exclude the Time-of-Day -- does that ripple through to the Crosstab?
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I agree with Ken about the axis formatting not affecting the crosstab output. You will want to change the Data Type for that date field in desktop and republish. To change the Data Type for that field in desktop, right-click on it, select Change Data Type and choosing Date (instead of Date & time).
This worked - the date was a calculated field though, so I couldn't change the data type directly - I ended up casting it using Date()
Thanks all for your help!!!