Stacy, what I found is that even though the Palette still shows up, empty, where you had it, if you use the Customize Palettes tool you will find that the Palette is not included in the Palette Group. It is, however, listed under the available Palettes. Drag that to the Group you want it in and it will be populated as expected. I'm not sure how to automate this.
What this means is that even though we can include the Palette in the .bundle, the user still needs to add it to the desired Palette Group. However, what this does allow is that you can make changes to the Palette and those edits should be reflected should be reflected for anyone using the bundle the next time it is loaded. Make sense?