icontakt
As for the selection issue in post #1, I can't tell until you post a video in which you zoom in horizontally (by keeping hitting Ctrl + right arrow, for example, until you can no longer zoom) at the start of measure 331. Clip Properties Inspector doesn't always show correct information.
Good catch. Looks like all my clips were aligned correctly, but somehow the marker is 2 milliseconds after the measure. I have no idea how that happened.