This message was added a few months ago, so if you updated your AFNI recently, you could start getting the message even in situations where it did not appear before -- because it wasn't in the program before.

Do you see results that make sense? The warning says that in any individual voxel, the strength of the statistics is weak. This does not mean there are no true multi-voxel (cluster) detections -- you can have valid clusters if you have a lot of weakly significant statistics right next to one another. That's what the various cluster-thresholding methods are for. With 3dttest++, you can use the new -Clustsim option to have the program do the cluster threshold calculations for you.