Hi Alfonso, 

Thank you for your reply. I can confirm that I am indeed using conn ver 20.a. I am importing my fMRIprep dataset via the following path in CONN's Gui: 

> Tools > Convert/Import > from fMRIPrep dataset > *selecting my fMRIprep folder*

Attached below is the file. To ensure I wasn't making a mistake, I re-ran the same procedures with the data that was fMRIPrep'd using version 1.5.4. Again, data from 1.5.4 imports covariates but 20.2.0 does not. I am happy to share the log file from 1.5.4 too, if you think that will help. As an FYI, both folders contain the exact same participants.

Regards, 

Nick