The AI to AE pipeline can be finicky at times if you don't know all of its quirks. There are a variety of things that don't transfer over, most notably opacity and blending modes.
If you imported layers at layer size and made any changes to the original AI file that would alter layer dimensions, the anchor point and position will technically be the same in AE, but will look different. You have to keep in mind that those properties are somewhat relative (position is dependent on anchor point, and anchor point is dependent on the layer size), so changing anything after the fact can lead to undesired results.
You said you haven't changed anything in the AI file, though.... If you re-import the original AI file into a new comp (let's go with document size this time, just to be safe), and apply some of the same effects... what happens? If you can get it working as expected like this, you might be able to do a quick rebuild by just bringing in the "broken" parts like this, and parenting them to the old versions (which have the right values, but don't look right any longer - correct?)
Do you maybe have another version of the same file (with same name) that AE might actually be linking to?
One other thought - if you're using precomps and the Collapse Transformations switch, that can lead to trouble, especially when mixed with certain effects. Is this the case? If so, it might be helpful to turn off all your effects, and troubleshoot one-by-one to see if it's actually one of those that's causing your troubles.
If none of these is the answer, would you be able to post some screenshots?
Hi Kyle, thanks for your response.
Because I was in the urgent need to finish the project the same day I replaced the graphics by turning them into vector layers within AE. Applying the filters, transitions and positions given from the original elements I managed to rebuild the file quite quick.
Unfortunately I can not answer your questions properly, since I don't have the original document anymore. But I think it is a thing with importing and the document size setting. Because I always had problem positioning the elements on their appropriate place within the canvas.
No worries. Hope your project turned out ok!
It always seems like these things rear their heads when you have the least time to deal with them...
Yes, always when you least expect it. But thank you very much for your help!