If you have aluminum or copper in the field it can cause beam hardning and show as higher KV
KV over spec
I am not a specialist on the 9900 but I suggest to check KV feedback signal. Somewhere in the control there must be an adjustment of KV curve linearity.
perform the generator mA Null calibration this calibrates the feedback readings and the HVSR board which should address the KV issue. this is a falling load type system so if your mA feedback signals are not calibrated correctly the KV will refelect it.
mA low KV will be high
mA high KV will be low
A little obvious but have you checked the power supplies, particularly the +5V.
There are a of offset (nul) current adjustments worth checking.
If you set manual kV and start low are you getting +15% through out whole range of kV's?