Well after playing around with the game behind the scenes, I've come to the conclusion that I need to completely rewrite the array based scoring system. It's just become too unwieldy. It was cobbled together on the fly, and due to this, it's started to become flaky as I've added new little things to the project. Ironically, a simple, simple thing brought me to this conclusion; adding the code to the next level button in the end level screen. This stupid, simple task has started making my shoddy score coding unreliable.
On a more positive note, I've added an enemy of sorts to the game. Till next week!