The context percentile filters for TargetScan analysis were moved from the workflow to the Options window and can be accessed and edited via Tools > Options > NGS > Small RNA > Target detection > Target Scan going forward from GeneSpring version 12.5.
 
The filters have to be changed in the Options window before starting the analysis to be applied. GeneSpring applies these filter settings to all subsequent analyses until you change them again in the Options window.