First make sure you are using your count field from the proper entity in the report, I forget if you get a choice for the report footer.

Use profiler and take a look at the query generated for the report. Run it to see the results that actually come back. I found that it was adding an extra join that didn't make sense and was bringing back the same set of rows multiple times. In my case I needed to add an extra relationship between the two tables/views in the data source view. Note, adding 2 relationships (with 1 column each) between 2 entities and adding 1 relationship (with 2 columns) between 2 entities can produce different results.

I also had to add a fake ID column (ROW_NUMBER()) as the results of my views and use that ID in the model for each entity's identifying attribute.

After both of these steps my number are always correct.