There is no boost in my PEQ table as it would be cancelled by the room anyway. I only use it to tame a 40Hz room mode (-9dB Q=2.5).
When using the highest setting in Surround Field "Maximum Enhancement" (even with no PEQ) I do see the clip protection come in occasionally, but it's only a dB or so and no audible muting takes place. The left channel intermittent muting which I refer to is not happening during loud passages anyway. It seems unrelated. My guess is that there's something awry in the Surround Field algorithms and it can only be a guess as I am not privy to them. It seems though that whatever is going on in "Surround Field", it spectrally colours the sound using L/R sum/difference algoritms with more "summing" going on (invoking occasional clip protection) with the higher settings. A different (allegedly non-colouring) approach seems to be the subject of Nokia's USP 6,928,168 in which only delay is used with cross-talk instead of L/R frequency-dependent amplitude sum/differences.
It's a minefield of patents out there and it's hardly any wonder that JRiver seems to play their cards close to the chest on this stuff. I would too.
This is no big deal as it only happens on some albums and rarely, but it actually sounds like the left speaker is switched completely off then back on again. And it only ever happens with the Surround Field in use. Maybe it's a natural side-effect.