How did you add the logo to your layout. Did you copy and paste it or did you use the insert menu? If you used the insert menu, did you click the "store a reference" option?
If you paste the logo or avoid selecting the "Store a reference" option, the logo (and your photos) should still appear when you copy the file to your iPad.
That was it. Once I unchecked the store a reference option it worked. Thanks for your help. I knew it was easy fix.