One common gotcha that I've tripped over even today...
If your fields are even one pixel too high, they'll be treated as though they are part of the upper part rather than the part you intended them to be part of.
Try selecting the fields in layout mode and then use your arrow keys to nudge them down a pixel or two. Then check and see if that fixed the problem.
I based the report on the Unit table
I believe it needs to be based on the Payments table.
PhilModJunk: No change. I even made the parts wide just to make sure, and there was no difference.
Comment: I tried basing it on each of the involved tables and the every other table (aside from Unit) gave even less information.
Comment spotted a detail I missed, you should base the layout (that's the show records from box in Layout setup...) on payments.
You also need to have list view selected and to have sorted the records in an order that uses all of the "break" fields listed in the SubSummary part setups. (Those are the "when sorted by", field.)
Also, if your copy of Filemaker is version 9 or older, you'll have to either preview or print the report before you can see it correctly formatted.
Place fields from Payments in the body part, fields from Wells in the sub-summary by Well part, and fields from Units in the sub-summary by Unit part. Make sure to find all the records from Payments you want to include in your report.