It's a long time since I worked on the CRJ900 Flight Test but we found a fuselage fundamental frequency would effect the IRS Vertical Acceleration (IIRC) term into the Autopilot. A High Pass Filter in the AFCS software around 3 Hz cured it. Might want to get your Maintenance people to check the IRUs are snug in their mounting trays and the mounts themselves. As neilki stated, the AHRS-4000 just isn't so sensitive to pick up the vibration. The same filter was retained for the CRJ1000 but both the 200s & 700s never needed it.