source/build holds the actual object files as they build, and the linked executables.
source/bin holds symlinks to the executables for convenience.
You should be using the files (linked to) in source/bin.
I’m not sure what you mean by “not completely created” – does scons report success or failure?
Finally, you should use “scons bin mode=release”, not “scons bin”, to get the optimized executables (they’ll run faster). Add -j# where # is the number of processors on your machine you want to use for multithreaded compiling.