I'm using Finale 2006 in Windows XP. I havent had this problem until recently. It seems to happen when I add a staff and create a new instrument to an existing template.
My noteheads in my template are changing at random. For example, I was inputting unison bass drum hits (supposed to be a slash) but the notes came up with ";Forte"; signs as note heads instead. I went to the map and saw that the Forte sign was on the template instead of the slash. That's just one example. Alot of different noteheads were different as well.
On this exercise I was writing, I had two bass line staves. One for unison and the other for splits. My unison line was fine. I added the second staff for splits and that's when I noticed the change. Both lines were using the same Finale map. When I clicked on the map for the first staff, it was fine. But when I clicked on the second staff (using the same map) the noteheads had changed.
Hope that's enough info. Let me know if you need anything else from me.