The LabVIEW timestamp format is capable of negative values - it is a signed, 128-bit fixed point number. However, its integration into LabVIEW is still not complete, so you occasionally run into problems like this. You can try the NI-HWS format. It was written after the timestamp was introduced, so should handle negative values correctly. You can find NI-HWS on your driver CD (all versions after fall 2004).
Why, you may ask, does the format handle negative numbers. There are two reasons. First, it was conceived as an absolute timestamp, and dates before Jan 1, 1904 do exist and scientists and engineers do use them. Second, it is also being used as a relative timestamp. For example, almost all relative timestamps from the NI-SCOPE API end up being negative. You have a third use case - not a timestamp at all. Be aware that is it a fixed point number with resolution on the order of 5e-20 and maximum value about 2e19.