Hi thanks for sending me the samples.
For me it is hard to tell if this noise is more prominent than with the original CPU. If you can, put the original CPU back in and make a direct comparison.
Since firmware version 1.03 (which you have), the noise floor is actually lower with the SH-1oh1 CPU (at least on the units we tested).
In order to get an idea what the source of this noise could be, I really need you to answer my question:
Does the noise floor change if you change the LFO speed?