Yes. Because you commited to only master, anything since the branch was first made is not included. Things like the memory leak etc aren't in the optimized branch.
I suggest you merge these fixes, and from now on commit to the optimized branch until everything is ready to go into master (in say a weeks time when no more optimization is possible :D).
On the plus side, with the SConstruct fix, it compiled, and it now working perfectly. Clouds are operational, slightly different, but overall the effect is the same.
When the test games wins, I'll send you the profiling results ASAP.