Oh, yes, we have discovered some situations where Animation Paper didn’t respect the EXIF data in jpegs, which could result in exactly this – imported jpegs comes in up side down.
This has been fixed for the next alpha release (alpha 4), but you can get the fix with this interim version here (for Windows): https://www.dropbox.com/s/kepx07jvceoqqqa/AnimationPaper_x64.exe?dl=0
Let me know if the problem is now gone?
Best,
Niels