These several workarounds have been posted by users here, I'm listing them together for use by all the community.
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Find the original png file in the project viewer, right click -> Modify -> Interpret Footage.
Under the Alpha Channel category, select "Conform Alpha Premultiplication To:
And also select the box: Premultiplied Alpha
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Haven't got time to go back though the thread to see if someone else has come up with this but the only way to fix it is to replace all of the .png files as .psd. Finished a TVC this morning full of .png graphics and animations. Saved them all as .psd and it's perfect.
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brought all my PNGs into After Effects and saved them as .MOV files with transparent backgrounds.
If you don't know how to save with transparent backgrounds, this was helpful: Quick Tip: Exporting with Alpha Channels in After Effects - The Beat: A Blog by PremiumBeat
I then brought the new MOV files into Premiere and put them in place of the PNGs. It was annoying to add the transitions all over again, but it worked! Deleting all PNGs from my project helped too. Anytime there was just one in the sequence, my whole video would render messed up. I too had a deadline today, and spent about 4 hours trying to figure out the problem. This was the best solution I could find for the time being.