Not at home so don't have SX in front of me now so please forgive any incorrect terminology...
There are two reasons why this might be happening.
1) Incorrect snap point on audio event: Each audio event has a 'snap point', which defines the location within the event which will be aligned with the grid when the event is either quantised or moved. The snap point is shown as a vertical line on the event with an 'S' in the middle. Normally when you import or create a new audio file or event the snap point is at the very beginning of the event but you can move it by dragging it, in which case the next time you snap or quantise the event to the grid, the beginning of the event will appear to be out of alignment. You can only see the snap point at certain levels of zoom, and you need to be looking directly at the audio event, ie. you can't see it in the arrange window if the event is inside an audio part. It's possible you may have moved the snap point without realising it.
2) Cubase has a bug: When exporting audio back into the arrange window it is vital to remember that Cubase does not always export the length it is asked to; in fact I'm not sure if it ever does. The way around this is to put the event inside a part as soon as it has been exported, and drag the end of the part out and back so you're absolutely sure it ends exactly on a bar (or beat, or whatever is most appropriate). Then when you duplicate the audio part many times you can be sure it won't gradually go out of sync with the rest of the track.
I think it's most likely that you've discovered problem 2) here...