As of r1942 (I don't know how long it's been in place), the -I- option is being passed on the command line when precompiling a header in the object output dir. As noted
here in the GCC manual, -I- inhibits the use of the directory of the current file directory as the first search directory for #include "file". This affects the include chains of popular libraries such as Allegro (where I first noticed it), such that any file in the chain whose directory is not in the list of include paths to search will not be found with a double-quoted #include directive.
This behavior is demonstrated by the attached project, in which the project SomeProject has a precompiled header which includes the main library header SomeLibrary.h. SomeLibrary.h includes SLAnotherHeader.h, which in turn tries to include SLYetAnotherHeader.h but fails. If the -I- command-line switch is removed, the command succeeds.
EDIT: Forgot to attach the file...oops[attachment deleted by admin]