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Fixed in 4.0.8. The code for font management in Windows was missing a key line that prevented it from loading additional fonts into the menu.
The problem was that fading an element out did not actually hide the element; it just left it visible, but transparent. I have fixed this so that now fading an element completely out also hides it. So go ahead and try it again and let me know if it works the way you want it to.
Please download the latest update 4.0.5 which was just released. This should resolve your issue. Let us know if you still have a problem.
I just ran some tests on my Retina Mini with 7.0.6 after deleting and redownloading the player from the App Store. I used both of your apps (Laura - I used the one you'd sent over for testing; Clint - I was using a version from a few weeks ago), and I'm unfortunately not seeing the performance issues you've described. I'm seeing it take about 1-1.5 seconds to go between pages, and reactions to taps are immediate (or nearly so).

We don't have an iPad3 handy, but we're going to get access to one next week and test again (just in case the faster processor in the Mini is masking the issue).

One of us will report back after we've had a chance to test on the iPad3.

It should also auto-update when you:

3 delete an element
4 add an element
5 change the layer for an element