Thank you for your replies, I have completely uninstalled FSL 4.1, then reinstalled FSL 5 first, then FSL 4.1. It now looks like the new FSL 5 script works (i.e. fsl_motion outliers -i "input 4d data"  -o "output file" [options]), using FSL 5 with the backward compatible script ((old version) fsl_motion_outliers "input 4d data" "dummy scans" "output file") still presents that strange behaviour (although it shouldn't); however I think I can live with it :-). 
Thank you again
Ale