My suspicion is this is actually what occurs for most of you, you just haven't inspected your own materials as closely (at max zoom on every 2 event boundaries). Maybe this is some automated way Cubase does things to make material chopped up in precise bars not sound so robotic? I don't know.
The only thing you said there that makes any sense at all is "I dont know".
I promise you that my bars start and end exactly where I intend them too.
Check these things:
Snap value set to Bar
Snap type set to Grid
Snap to zero crossing switched off
In transport bar where it says TEMPO it says FIXED
Now with scissor tool cut a bar of audio in the middle of an event and highlight it....in the info line it tells you start and end points and length which should read 126.96.36.199. Assuming that is correct drag that bar anywhere you like and drop.....check in the info line the start and end point is x.x.x.0 (i.e ends with a zero)....or you can zoom in as you have been and see if it lines up to 0.
i7 firstname.lastname@example.org, 12Gb, W7HP x64, Cubase 7.5.20 x64, Steinberg UR28M, Alphatrack, Wavelab Elements 7.2.1.