We have seen similar results before using the BioAnalyzer.  We generally see what looks like a carryover phenomena between samples when the chip is overloaded.  There are a few things to check.  First, make sure that the pins on the electrodes are clean.  We clean the electrodes in a sonicator weekly to ensure we get reproducible results.  Another issue might be that the chips were not vortexed properly, or perhaps the wrong chip was used.   How does the rest of the data look?

I've just started using the bioanalyzer, so I can't offer a solution based on experience. However, the attached troubleshooting PDF might be a good place to start, especially the section titled: Poor baseline: Drift. Cleaning the electrodes is a top suggestion.