Yes, if you allow the 1099s to be built with suspense activity included it will recognize that they were below minimum at the end of the year, but did receive a check earlier in the year.
The default 1099 processing is to create 1099s based on net. If you want 1099s based on gross you should check the box in the Misc options page of the Disbursement and JIB Options.
If you do not "Include Suspense Activity" when you build the 1099s, then the 1099s will show all money earned even if it is in suspense and never was paid to them. If you mark the option to "Include Suspense Activity" then the 1099s will not include any amounts that someone earned unless they were paid for those amounts.
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