It seems this issue is still there in 4.6.
Steps to replicate:
1. Created three different membership types for each of three different organizations (attachment 1)
2. Created a price set where each organization gives both a monthly price and an annual price for each of the three different membership types (the annual price being 12 terms of the monthly price) (attachments 2, 3 & 4). Our organization had options for recurring billing on the monthly payments, but it looks like that is not permitted in later versions (having the Auto-renew option active for a price set with membership options for multiple organizations gave me an error)
3. Registered four different individuals for different combinations of membership from the priceset.
The result was that the Bookkeeping Transaction report multiplies each persons membership payments by the number of memberships they signed up for. So for example. Elizabeth Adams, Felisha Bachman and Truman Bachman each signed up for a level of membership with each of the three Organizations, and in the report each of their membership payments are triplicated. Ashlie Blackwell-Olsen signed up for membership with two out of the three organizations, and her membership payments are duplicated in the report. (attachments 5, 6 & 7)
Since our bookkeeper uses this report to report on all revenue, she has to manually sort through and remove all of the extraneous instances of peoples membership payments. I would be very interested to see a fix for this problem. If you could suggest how much it might cost to fix this bug sooner rather than later, I might be able to scrape something together. It's either that or keep paying our bookkeeper extra for her time to sort through it!
Thanks.
Would be great if you can submit a patch for that and other reports. Most of the reports and other functionality were writtten before membership pricesets and hence will have an issue