I'm wondering why you are using the NTSC DV 24 preset. The standard for delivery now days is square pixels and h.264. Your problems could be caused by frame rate differences between the original footage and the render settings or by third party codecs that you have installed. Generally, as of today, if your system is up to date and your AE and Media Encoder versions are up to date most standard presets work just fine. Anything you are intending for playback on a mobile device or computer should be square pixels and h.264. DV and the other formats like AVI are a little long in the tooth and not very compatible with a lot of devices. DV codecs have lousy quality compared to multi pass h.264 MP4 files.
So make sure that you are up to date and provide some details if you need more help.
What plugins are you using?
Try rendering out of AE's render queue into an intermediate format (QuickTime with the PNG codec is an option) and then bring the resulting file into the Adobe Media Encoder to make your deliverable.