Yes! I came here for exactly this reason. I have several projects in Sonar which all use the same FX chain preset, where one of the plugins there is TSE BOD, and yet 2 projects sounded a lot quieter than the other 5 which shared the preset. I'm actually seeing peaks of 8dB to 10dB lower. And this attenuation comes from inside the plugin - in the 'loud' project, clicking the bypass button maintains roughly the same output level (as that's how I'd intentionally set it up), but in the quiet project, the output is a lot lower unless BOD is bypassed.
I had previously thought it was because I was accidentally mixing v2.0 and v2.1 across my projects (as they look identical in the UI, at least to me), but now after ensuring my comparison projects are both running v2.1, I can see that it is definitely a problem inside 2.1 (and maybe in 2.0 as well, not sure). It could be Windows-specific but it's not Reaper specific, I can say that much.
I will probably have to ditch the plugin if there's no fix for this soon.