Ignition
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Support Custom Icon Layouts
When inside of Ignition icons overlap.

Upon further look, it seems as if you have a different icon layout on springboard then it will mess with ignition. For example, i had 3x6 icon layout with homescreen designer in rotate view and that messed with ignition view. Also, if essential apps are hidden in springboard they will be hidden in ignition.
Not sure if there is a way to force those apps to be seen and force the springboard layout.
This may also be due to portrait orientation lock. Not sure I'll fix this, since the only way to fix it is to disable other tweaks, which seems awkward.