The dependency checker in v1.5.3 was extremely restrictive, and as such it creates exceptions where there are none. Basically what causes that is lines where more than one variable is declared, such as:
var xmin = 0, xmax = 0, ymin = 0,
ymax = 0;
The linker wasn't able to work with this pattern because no good regular expression could figure this out. v2.0 has a much more lenient linker and dependency checker which doesn't trip up on issues like this. I know it might be a lot of work to convert your game at this point, but I would recommend it due to the improvements in the engine and the much more lax engine linker.