Not always. If I can get a broken version and a non broken version using the same source code it should be a relatively straight forward process. it might take a bit of time, but depending on what is causing the issue, once you spot it you can work backwards to see where the problem starts, is it compiler, imports, build environment, logic error or a combination of all of them? It could even be an underlying problem with a windows component that is only exposed by building in a certain way and then performing a certain set of instructions.
This really is the same process as looking for esoteric vulnerabilities. Once you find a bug using RTA (there are lots and lots) you need to quickly be able to sort through.
Symbol information for both builds would greatly speed up the process too.
One caveat, it will take much longer if i have to use a kernel debugger - but at the moment i dont think that is necessary.
I will start profiling a build I have anyway. - once this is done the differential analysis should show the problem within a few hours. (if the builds match)