need more info on what you have. What kind of bike is this going on? How do you have the rack attached? How much sag are you running in your suspension? What size and how much pressure are you running in your tires?
Short arm, single pivot, linear motion suspensions are very good at soaking up very small bumps, but very bad at bigger bumps. those can make a black top toad feel smooth as glass but hammer your spine if you hit a rock the size of a wad of chewing gum.
Long travel, long arm multi link suspensions are great at soaking up huge hits, but are very sensitive to small bumps, meaning you may feel every pebble in the road, but not that Honda you just road over.
large volume tires really do great soaking up hits, but they can slow down the impact of a large bump enough so that the shock's valves don't cycle correctly and you feel larger impacts more.