If you use a flowjo v10.0.6 template, load multiple data files, save the analysis, then re-open the saved .wsp workspace file, the statistics in the re-opened workspace need to be recalculated to be correct.
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-NOTE the issue is fixed in flowjo v10.0.7. The Java programmers are working hard to finalize v10.0.7, but until it can be released, one can download and use the latest beta http://beta.flowjo.com/
In FlowJo 10.0.6, one can automatically force the workspace to recalculate the statistics when it is opened. First, edit the .wsp workspace file with a text editor, changing the flowJoVersion tag to 10.0.5. Then save, and re-open the workspace in v10.0.6.
(If the wsp xml version tag is set to a value other than 10.0.6, FlowJo v10.0.6 will recalculate all gates and statistics on open).