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It is a little hard to tell exactly what is going on from the screenshot -- but be aware that there is an order of precedence to formatting. Formatting at the sheet level trumps the default formatting of a field. Formatting at the row or column level trumps the sheet level formatting. So, I would check alignment for the field (the little drop down called "Fields" in the upper right of the format window), the rows, and the columns.
If everything fails, would it be possible to post a packaged workbook?
Hey Josh, sorry I didn't realize format needed to get so specifc! Actually, Patrick over at Tableau support was able to help answer this question. They are using pretty complex table calculations, which is why they are not automatically right justified as normal measures would be. The solution Patrick gave me, which totally worked... but is totally not intuitive is: go to the Analysis menu > Stack Marks > turn off.
Glad you got it!
Wow, I just wasted an hour on this same issue and finally looked here in the forum. This completely resolved my problem also as I was using complex table calcs.
Haha John, that has happened to me more than once! Glad you found this thread helpful. Not sure what is happening during the calcs that the alignments change though...