Scenario editor and extracted scenarios

So today I extracted the first malay scenario from the campaign to play around with it.

The extracted scenario seems to work find during the testing, with the exception of one detail, the increase to population cap entirely fails upon tower destruction.

One starts with a pop cap of 75 and this is to be increased by destroying towers in the scenario. However when extracted this no longer works, instead once a tower is destroyed and replaced with my color tower, if this tower is destroyed the pop cap decreases!

Anyone know what is going on here? It only seems to work in one direction.