Hello, you aren’t missing something. This (independently shuffling columns in a conditions file) isn’t a feature that Builder currently offers but is probably the most-requested upgrade we need to implement for linking conditions files to loops.
So for the time being, you’ll need to do this yourself, using code to do the column shuffling for you at the start of each experimental session. e.g. see this post:
Give it a go and come back to us with any problems.