Over a year later I came back to this issue and finally made some progress. I still do not know the root cause or whether it's an issue with Jasper, Excel or both; I've got a work around though.
New information: Noticed that in Excel, the cells that were changing color when printing had a color set to 'Automatic' instead of #000000 (Black), as defined in the report template. Also, cells where I had a conditional style resulting in a Red color were unaffected by the color change bug.
Work around to prevent this issue: I set my default style to have a forecolor of #010101 instead of #000000. This prevents the cells from having a color of 'Automatic' and prevents the color change when printing.
