I just started reading about the properties of the TDMS file format, and am getting nervous my data doesn't have timestamps. I have been acquiring data using this format for a week already. Right now I'm working on the code for the viewer executable. I thought for sure that TDMS saved a timestamp for every waveform sample, but after some reading I'm not so sure anymore. It sounds like it is dependent on your code. I'm acquiring my data from a DAQ device. I haven't had much luck using the "Get TDMS property VIs" to see if I have a timestamp for every sample or not. My samples aren't all at the same dt. I'm saving based on time and in the event of an alarm.
Without being able to see your code, and based on your description, it sounds like you should be saving the timestamp with every datapoint.
This is a good example of how you could do that: