Those file size differences are pretty modest -- they can easily be caused by changes in gcc (either the compiler or linker), or any of the libraries that are statically linked in. Most of those are bundled with VSP and would be the same, but they too are being compiled with the different toolchain.
The size difference might be explained by including debug information. I would have expected a larger difference, but that depends on the platform.
CMake defaults to a debug build. Unfortunately, debug builds of OpenVSP are far too slow to be useful. We're talking minutes for a single update of a Wing.
When developing, I usually use a 'Release with Debug Info' build. This gives the ability to run with a debugger (somewhat imperfectly) while giving nearly release speed. The official downloads are compiled in Release mode.
If this build defaulted to a true debug build, then it would have additional checks for things like vector limits -- and the bug you're seeing might be a real bug. However, I would still need a more complete stack trace and a test case to chase it down.
Rob