Still mucking around with the expanding board. I've stopped destroying an board instance and making a new one, and moved to modifying it. I may have to go back to the old way, but even after the previous modifications, I a few creeps were able to phase through the walls.
I've fixed that by only allowing one line of creeps on the board at the same time. This will have to change later, but it gets rid of the secondary phasing problem, which occurs when the AI delays get long because of the expanded map size.
These delays hold up the interface, so it looks like improving making the creep ai faster needs to be the next priority.