Unfortunately, I haven't been able to reproduce this problem. There's likely a step or two I'm missing here. What's the frame rate of your source footage? How did you create your sequences? Did you choose one from the preset list (if so, which one)? Did you use the "Create Sequence from File" feature, or create a Sequence setting from scratch? Same question(s) apply to the nested sequence. How were they created? I'd also like to get a look at a project that has this problem. Do you have a project file that you can send or post?
~ Mitch