The first thing to look at is multiple buttons that control the same function. You might, for example, have two buttons that control Loop 4. Those buttons might be on different pages. If, in a preset, you have one button on and the other off, then you might get unexpected results from Loop 4 - it might be on, it might be off.
One thing that helps avoid this is the IA Link setting. Turn this on for your buttons that control switcher loops - if you have two buttons that control the same function, turning one button on will also turn the other button on. This helps prevent the buttons from getting set to opposite states. This feature has its limits - it only compares the first action of each button to determine if they're the "same", so if you have complex buttons that do a lot of things it might not work for you. In that case, you'll have to check manually and make sure that all buttons are set correctly for the preset.
As for problem #2 - edit the Page / IA Store button. You'll see that it has Min and Max settings, which are set to 1 and 2. Set them both to 0 to remove the limits from the button. This is a new feature of the 3.0 firmware.