> Are you saying that you didn't have collinearity when analyzing each run separately but you did when the two runs were concatenated? If so, something was not properly specified in the latter situation.

Yes this was indeed the case. In my afni_proc for the concatenated multiple task runs this is what I used to define the model:

regress_stim_times ${subj}/afni_folder/B*afni_task*.txt \
-regress_stim_types AM1 AM1 \
-regress_stim_labels step stand \
-regress_local_times \
-regress_basis 'dmUBLOCK(0)' \
-regress_apply_mot_types demean deriv \
-regress_motion_per_run \
-regress_censor_motion 1.0 \

Let me know if anything looks off- task A in this case is step, and task b is stand.

Cheers,
gerome