To be sure about this, I'd need to know how much compression Night Mode applies. I'd also need to do some tests of my own. That being said, what you've posted might be TOTALLY normal. Here's why: You're looking at a linear view of the waveform. As you probably know, hearing (and most other human senses) are logarithmic. This is why the deciBel scale was invented; because it's a logarithmic representation of magnitude (Volume).
If you change the view in Audacity to Waveform dB, instead of Waveform, you'll see a more realistic version of what's going on with the files. Click the down arrow in the upper left corner of the track and select it.
I'm *guessing* that JRiver's night mode applies something like 10 to 15 dB of compression with a medium low threshold like -30 dB. If I'm right, you're going to see something like 12 dB of extra gain throughout most of the track, but the peaks will be unchanged, or affected only slightly.
Further, I don't see any clipping in your waveforms. Audacity normally indicates clipping with red indicators to make them really obvious. I understand you saying it looks very different and you probably just mean "turned way up" for clipping. But that's an incorrect use of that term. I point this out because terminology is important to me and for good communication in general. I've also talked to LOTS of people who use the term clipping to mean all kinds of different stuff that it doesn't mean. Anyway, just know that the waveform doesn't appear to be clipped.
In short, I think MC is doing it's job exactly as it's supposed to. But someone else here is bound to know more about this than me.
Brian.