I would guess (and it is a guess without the data) it could be the same problem we had on the message board about a month ago.
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afni.nimh.nih.gov]
Namely, the problem was datasets with "funny" numbers don't work well with the default settings especially when the "funny" dataset is displayed in the overlay. There are two solutions. The first is to check the data with either float_scan or 3dMax for those numbers. Then one could determine at what point in the processing these numbers occur. In that case, 3dToutcount generated the numbers, and it has since been fixed.
The second solution is to set an environmental variable to check and fix these numbers. Set AFNI_FLOATSCAN to YES. This won't really help find the cause, but it may avoid the crash.