As you can tell the shape tool always places my shapes at weird scale and not even. as if it auto warps my shapes and it is really annoying and I cant get my work done without my default shape tool.
Is your constrain angle anything other than 0?
Check your Preferences for that.
It is at 0 but it still does it.
Before resetting preferences, is the perspective grid on? View > Perspective Grid > Show/hide grid