Illustrator Import to After Effects

Hey all,
Its been a while since i ever had a problem with importing things, in fact its never been a problem until now, and no-one seems to know whats wrong.
+ i'll post links to images as well to fully show whats wrong.
Problem:
Im working on a project where i animate a character made in illustrator and then importing it to after effects. I made the character fine in after effects see here:
http://img.photobucket.com/albums/v77/nethstar/My_o_Fine.jpg
Then after saving it and importing it into after effects, some of the layers seem to want to move layer order or change shape, as seen here:
http://img.photobucket.com/albums/v77/nethstar/My_o_Bad.jpg
(As you can see the arm has gotten smaller, and the hand in the back is not layer behind the leg as it was in illustrator)
Im not sure what else to mention apart from, i've worked illustrator for the whole thing, there are around 57 layers and it is quite a complex layout but i managed to make everything work that wat previously with another project but for some reason this time it wont change. Ive also tried chnging the save settings many times but not really made any difference.
Im using CS3 versions of both Illustrator and AE.
If anyone could help i would be highly greatful.
Thanks in adance.
P.S: It works when i use a photoshop file but not with illustrator, but i find it less time consuming to work with an illustrator file in case ineed to make adjustments with the the character. ALSO i found that layer order does not stay when importing from illustrator. eg - Layer 1, 5, 2, 3, 6, 4, ordering in illustrator will come out layers 1,2,3,4,5,6...and its REALLY fustrating because tutorials seem to do it with ease.

Re: layer order: You may have some invisible stuff inbetween which could throw AE off track. Removing those invisible elements may improve matters. Also check your layer naming. Give your layers respective names to enforce correct ordering. Short of that - could be a bug, could be not. I'm doing not enough work with AI to gauge this.
Re: changes in size: This may hinge on the use of compound paths and clipping masks. There are a few known issues with this, some of which have been addressed in the 8.0.2 update, but not all of them. I'm afraid only CS4 will fully resolve the matter, so in the meantime you will probably have to find different ways to deal with it. One thing you can attempt is to disable the "Preview" option for at least one of your critical layers. This will enforce a different treatment of the file and AE will re-calculate the bounding boxes instead of using the info stored in the file for the preview.
Mylenium

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