I had this problem last year when integrating over to QBO from to desktop version. The problem was with HOW "Sales Receipts" were being entered. I am using the nonprofit version, so I go to +New > then under Customers, click Sales Receipt.

The way the previous treasurer was entering donor contributions, I believe, was from the deposit page. While you ARE able to enter the same information and generate reports with the same information, I found that it was omitted from the donor statements when I used the Quickbooks Advisor way (stated many times above). 

Unfortunately, I had to manually merge that year. I am doing it for the second time this year and the QB Advisor method now works for me. The only downside is that It doesn't breakdown receipt line items or specific funds, as someone said earlier.

We have over 50, but less than 100 members, so purchasing BRC's plan for more than 10 donor receipts is not worth it for me. If you want to invest in those types of software for years to come, make sure it offers QBO integration and great support. I have yet to fund an inexpensive one or one that will truly do everything I need it to for it to be a value. [If anyone has any ideas, please let me know.]

Some other suggestions, use Microsoft Word to enter bulk information through the Mailer tab. (Google it). Personally, I export a custom report (Sales by Donor Detail) to Excel. I break the master list down by giving each donor their own tab. I have not figured out how to make a standard few lines then customize the rest of the donor statement, but I know this can be done (requires more research/plug in/other software - again, if YOU know, please let ME know!). I do a whole document search and Replace "abcdefg" in the whole document to "abc" to make it esthetically pleasing and more simplified.

If anyone has a better idea for just 30-40 members, please let me know. Thanks! Hope this helps. =)