OK, I had a quick chat with @rsmith about this, the issue is that the problematic dataset doesn’t have a TotalReadoutTime entry for some reason. This is the information that constitutes the 4th column of the PE matrix – hence the error message.
The right way for us to handle this would be to insert some sensible default value in there if that entry is missing, but it’ll take us a while to find the time. A quicker fix for you would be to manually insert that information into your input DWI by adding it to the original JSON file (which I note is used in the initial mrconvert call). Alternatively, you can manually insert that entry during the mrconvert call using the -set_property TotalReadoutTime 0.0614 option (to match what’s in your other header). It doesn’t actually matter what that value is since your call won’t be calling topup (only one PE direction present in the data, so no scope for distortion correction here).
As to why this information is present for all other subjects, but not that one…? Not a clue, sorry… 