Allow pellets to air dry. Resuspend in 8ul of Formamide based loading dye. Allow to sit at RT for 5-10 minutes, with frequent mixing. Check your RNA for condition. Try RNasing longer or increasing the RNase concentration.
Sense template contaminating riboprobe.
Insufficent DNase digestion of riboprobe. There can either be premature stop sites in the probe leading to smaller probe sizes, therefore smaller products. This can also stem from overdigestion by RNase A which will break-up the duplexes if the concentration or digestion time is too long.