It's an, ummmm, undocumented feature. Amapi, unlike Carrara or the other programs, keeps track of the origin data of the file - where the page corner is in illustrator. Usually in Illustrator, the 0,0 origin of the page is in the lower left hand corner. So, when you import the file into Amapi, it treats the center of the Amapi work area as the origin of the document and displaces the imported art accordingly. Depending on the scale you've chosen to import at, it can be in the next universe. Here is how to fix it: show rulers in Illustrator, where the rulers meet there is a dotted cross, click and drag it to the center of your shape before saving or exporting as .ai v3. There is an advantage to "remembering" where the origin is. When building multiple shapes in proportion and scale with each other, but importing them seperatly, they will correctly position themselves to the others in the Amapi workspace. As for the compound path thing - it drives me nuts. It's an easy fix by selecting all of the paths that are the compounds and grouping and extruding them. Then you can simply subtract them from the other shapes but I wish you didn't have to go through that drill.