I struggled with this issue for too long before finally tracking down how to avoid/fix it. It seems like something that should be on StackOverflow for the benefit of others.
Found the answer here.
Basically, it's a problem with caching and you need to delete the ".data" file that is created in the same directory as your report. Some also suggested copying the query/report to a new report, but that appears to be the hard way to achieve the same thing. I deleted the .data file for the report I was having trouble with and it immediately started working as-expected.