Clang Library Detection Problems (perhaps related to Static Checker)

Hey all,
I am writing a custom static checker in Clang and I get an unexpected behavior with #include directives. Say I have a simple hello-world main.cpp source code that #includes stdio.h. When I compile a source file with clang without invoking the checker (e.g., clang++ -std=c++11 main.cpp), it compiles as expected. But when I call the checker: clang++ -cc1 -std=c++11 -analyze -analyzer-checker=myChecker main.cpp I get an error 'stdio.h' file not found.

My current work around is to call the first clang++ command above with the verbose flag (-v) and copy-paste all the flags the wrapper is passing to clang++ -cc1, but I'm wondering if there is a better approach. This approach is suboptimal because it prevents me from creating custom tests that are platform-independent (because the flags I copy-paste have paths that are specific to my computer). Am I for example supposed to provide any extra flags when I configure my custom LLVM/Clang build? In case this is relevant, I am building on Ubuntu 14.04 and configure without any additional flags. Interestingly, one of my collaborators is having the reverse problem. Library headers are automatically located when he calls clang++ -cc1, but not when the -cc1 flag is missing.

Am I configuring Clang/LLVM improperly? What am I missing?