I work for a membership association and we've run into the same issue when wanting to track membership as it stood each month. We're still currently working on it, but so far after meeting with our IT team we've considered one work-around. Rather than having the database on a live connection, we would pull monthly data extracts instead (Based on paid through dates, activity records, etc). Then all we would have to do is union each month and use the date dimension to show counts for each monthly extract. We should be testing this within quarter 3 of this year so I'll come back to this one and let you know. I figured I'd share in the meantime so you also a a chance to try it out. If you do- let me know if it worked for you!
I am very late to the party here, but just stumbled across your post. One work around here is ro review the merge used to join the historical excel datasets to the current Netforum dataset. This will alow you to control what fields are linked in the two datasets. These linking fields are what allows the filter to be applied over the two datasets.
If you are still experiencing this issue, I would be happy to discuss further.
All the best,