If you were using the R-09's internal mics, they were probably overloading. I'm guessing that maybe you were recording rock music or something similarly loud - those mics are really not designed to handle those sound pressure levels.
For recording music, you need to keep all of those limiters, low-cut filters, etc. OFF. But even if you do, you cannot stop those internal mics from overloading, because they literally do not have the sensitivity to handle that level of volume. Turning on a bass rolloff will not help, either.
I would recommend an inexpensive pair of external mics and a "battery box" or small preamp, and run that LINE-IN to the R-09HR with all of the switches off (except HOLD). That will virtually never distort. There are some Church Audio CA-1 mics in the Yard Sale that would fit the bill at $65. Those plus a battery box from Church or Sound Professionals (Sound Professionals is in NJ and, if you're taping in AC, probably close to you) and you will have a very nice sounding rig for less than an additional $140. Considering that your recorder costs about twice that, that's not much to invest in the hobby, and it will deliver considerably better results.