There are multiple solutions for this, but you should never disable Clipping Protection.
For one thing, all digital controls should be used as negative adjustments. I'd actually be surprised if JRiver doesn't normalize that behind the scenes.
What that means is, instead of boosting Bass +6dB, you would reduce Treble -6dB.
The effect is the same, but it won't clip/distort.
I'd also strongly recommend that you run audio analysis on your library - which may take some time if none of your files are analyzed.
You have to select all your tracks, and then use: Tools > Library Tools > Analyze Audio.
Once your tracks are analyzed, enable Volume Leveling in DSP Studio.
This should generally provide you with more headroom for DSP, and ensures that inter-sample clipping is also avoided, not just sample-based clipping.
You should also change the dither mode to TPDF rather than JRiver Dither if using Volume Leveling. Tools > Options > Audio > Advanced > Dither Mode.