Hi @pruittpj ,
According to the BIDS spec:
If several scans with the same acquisition parameters are acquired in the same session,they MUST be indexed with the [run-](../99-appendices/09-entities.md#run) entity:_run-1, _run-2, _run-3, and so on (only nonnegative integers are allowed as run labels)
I believe BIDS generally preferred run labels to have non-negative integers, but was agnostic if runs were zero-padded (e.g. _run-01). My impression is that the newer fMRIPrep versions are adhering to the BIDS terminology more strictly, hence the conformity towards non-negative integers for run number labelling.
Moving forward, it’ll be a good idea to not zero-pad run numbers when converting your data to BIDS, thus eliminating the labelling discrepancy between your input data and fMRIPrep’s output.