I've been working in Adobe's premiere and after effects for quite a few years now and this problem is new to me.
I'm working on a project in After Effects CS6 and want to import a premiere pro project into After Effects. I go -> File -> import -> adobe premiere project
Now After Effects CS6 imports all files from the premiere pro project like before in CS5, but now also imports the videofiles as sequences at the root in my project panel and messes everything up. Before it usually imported nice and tidy with the same folder structure as the premiere pro project would have.
But that isn't the main problem. When i open the sequence i wanted to import and work on, some clips have been shortened down to 1 FRAME LONG at the end. These clips have a 500% speed in premiere pro, but this has never been a problem before, after effects has always before been able to translate the speed variations in clips from premiere -> after effects.
The adobe premiere project that was imported is a 60 sec promo with various clips in various formats (Gopro h264, dv pal quicktime etc). Footage not exceeding the fair amount that after effects should handle. 15-20 videfiles at 30 sec each.
I've never had this problem before with premiere <-> after effects.
I just found the solution!
In my adobe premiere project that i was trying to import, some of the clips were "right clicked" and applied "Scale to frame size"
Every videoclip that had "scale to frame size" in my adobe premiere pro sequence would import as its own composition in After Effects rather than just a videofile, and some of the clips would be trimmed down to be invisible.
So if you have any problem with a clip not importing correctly into a sequence in after effects, check to make sure "scale to frame size" is not applied to the clip in premiere pro.
I removed the scale to frame size in the premiere project and now everything imports fine into after effects.
Sorry for the post.