You don't show your timeline, is it a one frame with a movieclip that has the 5 seconds of animation, or is the animation on the main timeline? Are there any stop(); actions in it?
Assuming you are getting a 5 second MOV, don't send it to Adobe Media Encoder, use the MOV in Premiere. The black background is normal for something that has an alpha, but in Premiere you will need to right-click on the media in the project panel and choose Modify/Interpret Footage. In there make sure the Ignore Alpha Channel isn't checked. There are also settings for whether the alpha is premultiplied or not. I haven't tested that, but I suspect Animate is premultiplying. Try different settings to see which one gives you the cleanest edges.
You could send the MOV through AME, and your settings are probably right, but you're adding another thing to go wrong, and lowering the quality, to save a bit of drive space.
Thanks for your help. Below is a screen shot of my timeline. No stops or actions - I don't have a clue how to do either of those yet. I was finally able to get a sorry workaround by using the export PNG feature. I would like to figure out the best way to export/import high quality animations for final assembly in Premiere Pro. Please let me know if you need any additional information.
Thanks again - Ben
There was no screenshot attached. What I said in my previous message is what you should do. Export to MOV, don't convert to MP4, and in Premiere interpret footage and make sure the ignore alpha is not checked.