Suggestions:

(a) click on one of these new active voxels to make it the focus of the crosshairs, then write down the value of the threshold at that location in +tlrc view. Then switch back to +orig view; the cursor should remain in the same anatomical location. Compare the value of the threshold in that +orig voxel and its neighbors to the value you observed in +tlrc coordinates. The value in +tlrc coordinates should be comparable to one of these -- if it is very different, something is wrong. You can see the current voxel's values at the bottom right of the Define Overlay control panel.

(b) open the Define Datamode control panel while you are in +tlrc view; switch the 'Olay resam mode' and 'Stat resam mode' to 'Li' from the default 'NN'. This will tell AFNI to use (tri)Linear interpolation instead of Nearest Neighbor interpolation when displaying in a transformed coordinate system such as +tlrc. This change usually gets rid of isolated activations and sharp corners in large activation blobs.

(c) if you are still unhappy with the situation, you can upload the offending dataset (SPGR and functional) to here for us to take a look at it.