Aspect ratio and pixel aspect ratio are two different things.
Aspect ratio is the ratio of your entire image. Pixel aspect ratio is the aspect ratio of a single pixel within that image.
To find the pixel aspect ratio take a look at your composition settings. Since your working with a custom setup working in square pixels only would probably solve your problem (unless you have some reason not to be)
Non square pixels (ie anything else) always need to be converted to square pixels to preview properly. This is what your doing in Photoshop when you enable the pixel aspect ratio correction. Im guessing this is where your running into problems but without knowing the pixel aspect ratio's your working with it's hard to tell.
It could be that you just don't have the pixel aspect ratio correction turned on in after effects. it's the small box with double arrows over top of it underneath your composition preview.