If you're using LabVIEW to read data from the file, you can just wire the channel names for "TDMS Read" accordingly (array of strings with the first element being the name of the time channel). The order in which the channels were stored wouldn't matter then.
DIAdem, Excel, TDMS File Viewer and others however will display channels in the order in which they were stored. If that's what you're using, you can create the time channel first thing after creating a new file by calling "TDMS Set Properties" and setting a property on that channel. TDMS Write will then add all new channels further down the list (side note: if you are using the "NI_MinimumBufferSize" feature, you need to call "TDMS Flush" after setting the property).
Hope that helps,
Herbert
