The fact that the problem only occurs in the treble region would seem to suggest that it is arising in circuitry within the JD9 that is "ahead" of its RIAA equalization function, or that perhaps involves the RIAA equalization function itself. That function attenuates the treble content of the signal provided by the cartridge, the amount of attenuation increasing as frequency increases, compensating for a boost that is introduced in the recording process.
If you don't have any spare 12AX7's to try in the JD9, it might be worthwile to simply try interchanging the two 12AX7's between the two sockets. Even if that doesn't fix the problem, if it results in a significant difference of any kind it would suggest the possibility of a bad tube.
Also, you might try working each of the six gain select switches back and forth a couple of times (while the system is turned off!), in case there is some marginal defect in them that might be causing one of the MC gain settings to be inadvertently selected.
Also, consistent with some of the comments by ZD and Mofi I'm surprised that you have found the high output jacks to be preferable to the low output jacks, given the relatively high output of your cartridge (5.5 mv under the standard test conditions, assuming that the cartridge is a 2M Blue, not a 3M Blue as stated), and given the unusually high gain of the JD9 MkII (60 db in the MM position, which I presume applies to the high output jacks, and if so would correspond to about 49 db at the low output jacks, which is still very high). (The original version of the JD9, btw, was spec'd as having even higher gain, 70db for MM's as Mofi noted).
Finally, I see that your integrated amp has an input sensitivity spec of "370 mv to 3.0 volts rms." That would seem to imply that its sensitivity can be adjusted, although the manual doesn't refer to any such adjustments. If it is in fact adjustable, however, and it is presently set to the lower (more sensitive) part of that range, and its volume control is not located at the very front end of its internal signal path, it is certainly conceivable that the high gain of the JD9 coupled with the relatively high output of the Ortofon would overload whatever circuitry in the amp is "ahead" of the volume control. You might want to contact Simaudio and ask about the meaning of that spec, and if input sensitivity is internally adjustable.
Just some thoughts; hope they help. Regards,
-- Al
If you don't have any spare 12AX7's to try in the JD9, it might be worthwile to simply try interchanging the two 12AX7's between the two sockets. Even if that doesn't fix the problem, if it results in a significant difference of any kind it would suggest the possibility of a bad tube.
Also, you might try working each of the six gain select switches back and forth a couple of times (while the system is turned off!), in case there is some marginal defect in them that might be causing one of the MC gain settings to be inadvertently selected.
Also, consistent with some of the comments by ZD and Mofi I'm surprised that you have found the high output jacks to be preferable to the low output jacks, given the relatively high output of your cartridge (5.5 mv under the standard test conditions, assuming that the cartridge is a 2M Blue, not a 3M Blue as stated), and given the unusually high gain of the JD9 MkII (60 db in the MM position, which I presume applies to the high output jacks, and if so would correspond to about 49 db at the low output jacks, which is still very high). (The original version of the JD9, btw, was spec'd as having even higher gain, 70db for MM's as Mofi noted).
Finally, I see that your integrated amp has an input sensitivity spec of "370 mv to 3.0 volts rms." That would seem to imply that its sensitivity can be adjusted, although the manual doesn't refer to any such adjustments. If it is in fact adjustable, however, and it is presently set to the lower (more sensitive) part of that range, and its volume control is not located at the very front end of its internal signal path, it is certainly conceivable that the high gain of the JD9 coupled with the relatively high output of the Ortofon would overload whatever circuitry in the amp is "ahead" of the volume control. You might want to contact Simaudio and ask about the meaning of that spec, and if input sensitivity is internally adjustable.
Just some thoughts; hope they help. Regards,
-- Al

