"Use motion synchronization mode", this is still experimental. The idea is that instead of synchronizing the videos on a common event by shifting one in relation to the other, this mode uses the length of each video segment and changes the playback speed of the right one, such that both the start and end are in sync (but they are no longer using a comparable time base).
Basically it's a way synchronize a whole segment by scaling the time axis in addition to translating it. This can be helpful if you want to compare form within a larger motion while doing abstraction of the performance speed. For example say we have two long jumpers and we want to compare their form during the aerial phase, but one jump is taking longer than the other.
Regarding cameras that have the same name. In the log there should be a line with the camera identifier. This is normally a unique name, it's the DirectShow name. I think I've heard about this issue with the Kayeton cameras. Can you check in the log if they have the same "moniker"?
