If you are using the Bionalyser please refer to page 29 of the RNA 6000 NanoAssay protocol guide (Cleaning up after the RNA Nano chip run) and ensure you have run through this cleaning protocol before you leave the machine. We had a couple of problems last week probably caused by dirty electrodes.
Basically pop in an electrode cleaner with 350ul RNase-free water, close the lid, wait 10 seconds. Open lid and evaporate water off for 10 seconds. Remove cleaner.