When I took the Smart Device board to get FCC/CE emissions certification, I adjusted the swing level voltage settings myself to reduce swing, and hence, reduce the amplitude of the radiated frequencies.
Its can all done by register settings, and it is explained in Appendix A, section 34.8 of the reference manual. Except, I see that one, rather important calculation, was left out of later revisions of the reference manual (probably because it confused too many people):
So basically, VPHrxterm is determined by the receiver side pull up voltage level, which should be 3.3V. If PREEMPH is zero, then VHI will be the result of the third term in the equation above. The higher the resistor value chosen in 0x19 d_tx_temp[2:0] (which is RTERM), the higher VHI will be. I would recommend a value of 133 Ohms. What is the value being used in the Electrical Specification test?
You can assume a value of RXTERM of 50 Ohms for the receiver side.
Once you get VHI up to help it up over the missing corner of the eye test, you can adjust swing voltage to make sure the bottom edge clears by adjusting TXLVL and CKLVL. The lower the value equates to a higher swing voltage.
So to recap, you definitely want the following register settings:
0x19 d_tx_temp[2:0] = 101b
0x09 tx_symon = 1b
0x09 tx_traon = 0b
0x09 tx_trbon = 0b
And you might want to start with:
0x0E sup_tx_lvl[4:0] = 10001b (17)
0x0E sup_ck_lvl[4:0] = 10001b (17)
and adjust those numbers down if the bottom corner is now out of spec, or adjust them up if the top corner is still out of spec.
Please give this a try and let me know the results if it does not work for you.