I know I've done this is the past . . . have an mxd with a layer thematically displaying based on values in a spreadsheet to which it's been joined. When I publish, the joined fields are gone, as well as the rendering. Just applied SP4 to both ArcGIS Desktop (View) and ArcReader. Any ideas? Here's my data: http://www.arcgis.com/home/item.html?id=2b434536ec9f4ec5a67f02509ea2c36f
In doing some testing with the information provided, I also have 10.0.4 (ArcMap) and I was unable to reproduce the issue you are seeing. I would like to work with you on this issue, so if you would submit a webform and add my name. We can have a incident created and then trouble shoot this issue together. Gracias!