I've only had one MPX-100 come across my desk, and while I didn't measure it's response characteristics, neither was I drawn to any obvious difference in audible performance versus that of the countless sub-chassis adapters I've seen. Both versions of the MPX-100 and the MPX-200 use identical second order de-emphasis filters that operate in a dedicated, active stage for de-emphasis tailoring. Early MPX-100s use discrete components, while later MPX-100s and the MPX-200 use the same PEC component for the de-emphasis filter.
On the other hand, the sub-chassis de-emphasis networks are entirely passive, so to make up for the loss of the active element that the stand alone units employ, the sub-chassis units employ a notch filter to effectively eliminate the 38 Khz sub-carrier from the output. The response of these units I have measured, and while not perfect, they are darn good at what they do even though they are a passive design, thanks in large part to the notch filter they employ.
So to answer your question, I don't know of any issue with the de-emphasis networks in your MPX-200, but it wouldn't hurt to check as many component values within it that you can, and maybe even build out the filter in one channel with discrete components, and see how that differs from the other channel still using its PEC network.
I hope this helps!
Dave