Just so i understand are you synching the HD clips (which are segmented...not continuous...and or have breaks) each into its own SD counterpart OR synching all segmented HD clips into the proper position and then making one long SD clip for each angle? If Yes, and your having trouble with playback of the HD clips, it seems that synching at that point would be problematic.
I line up all the segmented clips that make up one angle, synch them to my audio, and then encode one SD 720X480 .avi file. When I work with just one HD angle, the stuttering isn't too bad, so I am able to do a fairly accurate job with synching. It's when I stack up several HD angles that the stuttering gets to where I can't do my work. Of course, there are gaps between some of the clips - but I don't worry about them. They just shows up as black screen. I leave the original audio intact (but muted) when mixing (although I've already deleted the audio in the project in the picture below as the mixing is complete), and since there is no video/audio in those gaps, it's easy to see them because the audio below those gaps will be a flat line.
I start the proxy file for each angle at the same point where the audio I'm going to use in the final project starts. So if the angle doesn't kick in until 30 seconds into the show - that angle will start off with 30 seconds of black screen. The key to this is that I don't have to worry about establishing a cue point OR worry about something accidentally sliding out of place - as every proxy angle starts at the 0:0.00 second point on the time line. If I notice something is out of whack with the synching - it only takes a second to get it back where it's supposed to be.
After encoding a proxy file with the original segmented HD clips for one of the angles, I group the clips for each angle into a "group" so that the gaps don't accidentally get out of synch. I then move them off to the far right of my project - on the same timeline as their corresponding proxy file. I like to line them up starting at the 2 hour mark of the timeline (if the show I'm working on isn't longer than two hours). This way, if I discover something out of the synch while working with the proxy files, I can easily go back to the out of synch HD clip on the right side, ungroup the clips, make the (typically minor) adjustment, and then regroup the clips. It's easy to find which clip - because wherever it occurs on the left side - I just add two hours because the HD clips start at the 2:00.00 mark. Of course, this results in two cuts in the proxy clip - but it's actually fairly rare and one or two cuts in the proxy clip does not make it unmanageable.
Here's a visual example of how I do it. The 720x480 SD .avi files are on the left side and all mixing is complete. I know the actual cue points for the HD clips on the right. So after I delete the clips on the left side of the timeline, I will slide everything on the right side to each angle's beginning cue point, and then encode as an HD file.