Problems with syncing audio to video using merge tool

Question

I ran into a new problem that I have not had.
The project was shot on 35mm and transfered to 1080p 23.97 10bit uncompressed. I took the file in to FCP and through media manager maid a copy of it to ProRes 422 HQ 1080p.
The Problem is when I broke the clips up for each scene and take (like I usually do) and set my IN on the clapper and my IN on the audio file for that take at the sound of the clap and go to merge clips on IN points. The clip merges but not at the points I told it to. The audio gets shifted down or up by a good few seconds.
Why is this happening?
When I take the footage with the same IN mark and put it on the time line and the Audio with he same IN mark and put it on the time line it matches up. But not when I merge clips. I cant think what Im doing wrong if anything since this is the first time I have had this issue.
Thanks to all!

Answer 1

I don't think FCE has a multi-cam function like FCP does ... so here's another way to do it (if it does have a multi-cam function, disregard this).
• Place the clip you'll likely to use most on track V1 (along with the audio on A1, A2).
• Place the other clip on V2 (audio on A3, A4).
• Double click one of the clips to load it into the Viewer window.
• Play the clip until you find a good sync point (either visually or audibly).
• Place a marker at that point.
• Double-click the other clip to load it into the Viewer and find the same point on that clip.
• Place a marker at that point.
• In the Timeline, line up the two clip markers - it will help to zoom in to make sure they're perfectly lined up.
• Once you have the two clips in sync, double-click the upper clip to load it back into the Viewer.
• Click on the Motion tab and use the Scale and Center controls to get a picture-in-picture effect.
• Back in the Timeline, unlink the audio and video from both clips.
• You can delete the audio clip that you don't want to use.
• In the Timeline, as you're going through the footage, cut out the parts of the clip on V2 that you don't want using the Blade tool.
• When you're done, select all clips remaining on V2, right-click on one and select "Remove Attributes" then choose Basic Motion (all clips will go back to full size and centered).
• If you want to consolidate all of V2's clips with the clip on V1, select all of V2's clips, then holding down the Shift key, drag the clips down to V1.
• At this point, you can use the Roll tool to tweak your edit points if needed.
• Add transitions as desired.
This will only work if both clips are continuous (camera did NOT start and stop during the take).
-DH