If you used a different Nano to upgrade to the KD8CEC software, then you will need to recalibrate. The calibration data from the factory is stored in the EEPROM, which is not saved/uploaded with the software. Also, each board set is different, so you need to recalibrate anytime you change the Nano for a given board.
I would start with the BFO calibration to verify that it is correct. I have used the following webpage with Chrome and a USB (or laptop) mic:
You want to adjust more towards the "high" side, as that reduces any carrier bleed through. Note that the BFO should be close to 11.055500 MHz, as the SSB filter is 11.059 MHz. For my board 11.055600 MHz was about right.
There is also the Memory Manager software from KD8CEC that I have found useful in being able to save the current settings prior to making changes, then to save again as I get closer to what I want.