I am currently working on designing a digital magazine intended for the iPad 3.
When I design my psd working files at 1536 x 2048px at 300 ppi and then place them in the indesign file they appear to be about half the size that I would think they should be. So I exported the page as a PDF from indesign and then opened it in photoshop. When opened it's dimensions were 5588 x 7453 px at 300 ppi. So I saved this and placed it back in indesign and it appears to fit correctly.
This seems funny to me as it ends up being larger than a print publication. It ends up being around 21" x 29".
I know I must be doing something wrong but if I could please get a little bit of help it would be great.
I guess my basic question is how should I set my psd files up when designing for the iPad 3?
It seems like you are having some trouble with your ppi settings. If you are going to be designing for the screen (e.g. iPad, web) you need to use 72ppi. It may seem a bit odd as the iPad's actual ppi is significantly higher than this, but thats just the way it is. If you change your settings to 72 ppi, everything should go back to normal.
EDIT: Bob Bringhurst explains the difference between effective and actual ppis in this thread here: http://forums.adobe.com/message/4319794#4319794