Hi - in short I'm not sure what is wrong. I assume you are measuring the DNA based on fluoresence (plate reader)?
The excess "DNA" may be from background fluoresence from unbound dye.
This paper here (which I have not read) mentions that pico green and Heparin give a fluorescent background:http://www.babonline.org/bab/036/0013/0360013.pdf
If you are using a plate reader you may need to "blank" it against a well containing the heparin/pico green solution that you use to release the DNA (without DNA present).
Sorry I can't be more help