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I am seeing behavior in the new version in which projects that contain PNG sequences seem to lose those sequences, giving this dialog for every g..d... piece of media. I can cause the error by simply tabbing to another app and then back into AE. Note that projects open fine with all media and if you dismiss these multiple warning dialogs, everything works fine (of course for some projects, that can be hundreds of dialogs).
The error seems to disappear if you turn off Auto Footage Reload (hey, who needs features anyway?).
Windows 10 Fall Creators Up to date 256GB Ram All SSD or m.2 Nvida 2 Titan X Pascals 2 1080's.
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I have the exact problem on Windows 10, suddenly, with AE 15.1. It won't stop, it keeps asking, in a sequential string of dialogs which much be dismissed one by one (not for fun), and then they all reappear again when you least expect it. It makes AE useless for work.
It is like I'm being punished for writing this love song to after effects "After Effects, I Love You" Music Video by Joe Sparks (Country Song) - YouTube
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AE's error-handling subroutines are a nightmare if they catch a repeating condition; a half-decent program would have a "do not show this message again" checkbox on the popup, but Adobe prefers to let you click the screen a thousand times.
The PNG library seems much less stable than it used to be, and not just in this week's update. I've been seeing a load of entirely random PNGIO errors (CRC, header, etc) when reading frame sequences but the PNG files themselves are perfectly OK and bitwise validate against the originals on our media grid. One day it will read a frame, the next it will be convinced it's bad. Which frame it spits out is never the same. Restarting AE gets rid of the popups for a while, but I have yet to work out why it's falling over. For our longform projects that are still in Adobe software we've switched to always exporting as a frame sequence, because AE can't be trusted to complete the job in one go.
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Have now secondary confirmation. New version of AE loses PNG sequences when Automatic Footage Reloading is set to All Footage Types. Is reproducible. Happens after AE loses focus (for instance after rendering or going to another app and back again).
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This bug now seems to be confirmed by Adobe. May be Windows only.
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Hey, folks, I ain't havin' NO problems with my fully-updated version of CC 2017 -- it has all the bug fixes it's going to get.
If you don't NEED the new sparklies in CC 2018, think about reverting.
If you just enjoy being on the bleeding edge, deal with the bugs and welcome to the Adobe Unpaid Beta Tester Program.