Hi there,
I’m sorry to hear you never got a satisfying answer, since I’m having a similar problem and was looking for a sollution to.
I’ve been working with After Effects for over 10 years now and I’m now having this problem. It’s a new thing that didn’t happen with older versions: Sometimes while working you move your footage files to another location or change their folder name and your files in the aep. need to be reconnected. Only now it see’s the first file as an image sequence, which it shouldn’t!
I’m sure this did not happen in older versions of after effects so I’m afraid its a bug in the software, hopefully they fix it soon in an update.
You can’t check or uncheck the image seq. checkbox in this case, so there’s nothing you did wrong, just so you know!
kind regards,
Anne