Not being a Matlab person, I know a bunch of my colleagues have had issues with Matlab and TDMS.
I believe the issue is that you have "raw" DAQmx TDMS files. The data is written in raw form but scaling information is added. In LabVIEW, a TDMS file like this is seen as data in double type, that is, not even LabVIEW can recover the raw integers, just the scaled double data.
My guess is that Matlab is having problems applying the scaling information.
Sorry I cannot be of more help. Look below at the properties from your file, multiple scales.