If you have a link that seems to suffer from BER or packetloss/low throughput when running at a high modulation like qam256, but has good MSE (-32 or better) and runs fine at a lower modulation (like qam64) there is a chance the problems may be due to noise on the DC power line. You can test with loopback DIG to see if the problem continues (to pinpoint which side may have the problem), but you will need to take the link down to do this.
A ferrite should always be installed on the DC power wires just before they are connected to the IDU as detailed in the manual and in this Power Wiring FAQ.
First, turn off the far side opmode (if possible). If not possible as you wouldn't be able to turn it back on, turn off the odupower on the local side to minimize the signal coming in. If you are still seeing a strong signal, you may need to physically disconnect the IF cable going to the ODU, as any signal coming into the IDU could interfere with the test.
Next, disconnect or disable the Ethernet ports as enabling loopback mode will cause all traffic to loop in the IDU.
Then, set loopback mode to loopback DIG. You should have a link lock with an MSE of about -40. Ignore the RSSI as MSE is the only thing that is accurate in loopback mode.
Now, test with different speeds and verify with linktest if you are seeing BER. You may need to change the datapattern or inject some Ethernet traffic in order to calculate BER. If you continue to see BER at the higher modulations, this is likely due to noise on the power lines.
When done testing, set loopback to off, re-enable the Ethernet ports, connect the ODU, turn ODU power back on and enable opmode on both sides.
I know you'll have to find some scheduled downtime to do this testing, but hopefully this will point to the problems and help resolve them.