I have to use merged clips to sync video and audio because making every clip a sequence is too cumbersome and doesn't give me thumbnails to help choose my shots. Apparently, merged clips are very buggy. I can't use colored markers because they don't get saved on merged clips. I can't use match frame on merged clips because they don't find the correct frame. I can't set a poster frame on a merged clip except with the "in" marker. Are all those problems bugs, or is there something wrong with my specific system. I trashed preferences to fix another problem unrelated to merged clips, but that didn't solve any of the clip problems.
I don't believe there's anything wrong with your system.