Hi Ken,
I’m an Illustrator guy (been in prepress for years), and so I try to bring a lot of things into AE with AI if I can… these *may* be answers, or I may have to see a file…
1. Layers not in order
I’m assuming that you did frame animation, and each layer (above) is the next frame. Did you rename the layers? If not, do you see behavior where frames 1-9 are out of order (bad, but normal computer sort)in addition to other layers. I mean, if your highest level of layers is 3 digits, does it seem to sort correctly if you think about 1,10-19,2,20-29,3, etc? If so, then you need to name your layers differently (I think there’s a javascript out there, with a little searching). Of course, none of that *should* matter, but describe in more detail exactly what happens in AE. I use both platforms, and am currently on a PC, but am unable to replicate this error.
2. Changing dimensions
That’s the “cropped layer” choice. Don’t pick that. I would also assume that you’re copying the layer you’re working on making an adjustment, ad nauseum (that’s the way I’ve done it). Next time, I recommend on your start layer making a rectangle the size of your comp (I use 720X540), and making it a crop box which propogates to each succeeding layer; AE likes that.