There are some other threads about pops, maxed out meters, no sound, VST3 plugs, 64 bit engine etc, and some of these symptoms are what I see when I have my buffers set too low.
I've always blamed the MOTU drivers for this, since things work fine when I set the buffers right. Also with these newest drivers, I was having problems on some files when using buffers = 64, but I could change the MOTU buffers to 128, and it worked fine - then when I changed back down to 64, it continued working fine.
I've been working with MOTU support, and not much happening.
Now the breakthrough! I disabled the 64 bit engine in Preferences -> Driver settings - and voila!! All my files load fine at 64/48 and 64/16! I still can't use buffers = 32, but if I disable all plugins, it's fine. So I think this is a SONAR (with some VST3 plugins) problem after all. I think the bakers are on to it (according to the other threads) so in the meantime - I'm finished scratching my head.
I think I can finally say that these newest drivers are really good. ;-)