ChIP- Different DNA size for Input DNA and ChIP DNA on Agilent Bioanalyzer - (Jun/01/2011 )

I ran one of my input DNA and all my ChIPd DNA on Agilent Bioanalyzer today.And I am getting different DNA sizes for my input and ChIP DNA samples.Input shows a distribution around 100-300bp while ChIp samples is distributed around 900-6000bp. I processed them together ,decrosslinked overnight and cleaned up using Qiagen PCR clean up kit. I diluted the input 360 X to get 100pg/microlitre and the ChIPd DNA samples 10X to 300-500pg/microlitre before running on the Bioanalyzer. I am using Agilent High Sensitivity kit which expired on 3rd May 2011. The ladder ran correctly. So I am not sure if this inconsistency is due to the kit.
What could be the reason for this difference?

http://i55.tinypic.com/2prwgba.jpg
ChIP DNA Sample

http://i55.tinypic.com/a5jn1v.jpg
Input DNA

This is weird. It seems that something in the ChIP DNA sample such as protein is affecting DNA migration.

pcrman on Thu Jun 2 05:08:04 2011 said:

Thank you for the reply. I treated it with Proteinase K and cleaned up with Qiagen Kit. But it still looks the same.