Hi, Lucas,
 
You can accomplish what you want by using an exclusion mask from a simple baseline comparison of groups in the SPM GUI.  Run a simple CONN baseline comparison of groups (i.e., [1 -1][1 0]) and set your threshold a bit more liberal (i.e., p<0.005) and then save any resulting blobs as a mask image.  Then, run your desired group x time comparison (i.e., [1 -1][1 -1]) in CONN and threshold appropriately.  In the results window you can click on SPM view and then when the SPM GUI results pop-up it will ask you if you wish to mask the results.  It is here where you would select your ROI/mask from the [1 -1][1 0] group x baseline contrast and select exclusion.  This will then show you which of your results from the group x time contrast were not a result of reasonably significant baseline differences.
 
Hope this helps,
Jeff