Frame Accuracy Issues

I have looping animation projects that sometimes need to be produced in different aspect ratios and synced across multiple displays. I have been running into an issue where, despite the work area and frame count being equal, they don't always match up: One is often off by a single frame, which makes the synced videos out of sync after a while. A co-worker says he has also encountered this issue in Premiere Pro. In fact, the way we have found the frame issue from After Effects renders is by pulling them into Premiere and seeing the time difference in the Project panel or zooming in and seeing the discrepancy in a sequence. Does anyone have this experience and/or thoughts on how to avoid it? Again, everything APPEARS to match exactly from render to render. Thanks!