I think i should give some more details about my platform and project.
I am running on basically stock CentOS, every package comes from the official CentOS or EPEL repositories, the only exception are CodeBlocks and some libraries the project uses like boost, these i compile myself. So as of now i'm using gcc 4.8.5 and clang 3.4.2.
The project is not some testing playground but a real-life application which i am working on for multiple years now. The workspace contains 12 projects, according to the CodeBlocks statistics plugin around 570 files, 140K lines with 80K lines beeing code. There are no search path issues, the workspace compiles and runs fine, the integrated CC has no problem with boost. I'm pretty sure the problem is not related to the compiler configuration, but for the record, the include paths are comprised of absolute paths, relative paths and paths containing CodeBlocks Global Variables.
My VM was indeed running on only one core so i added another one and gave it another shot with a clean source tree. This time CodeBlocks was much more responsive during the initial parsing phase and after about 5 minutes the CPU load dropped to a normal level. However my problems are still the same and the toolbar doesn't seem to get populated faster.
It's not a general problem that boost doesn't get detected, other files using boost don't show the error, and i don't think its related to boost at all. I think its related to the fact that my includes are ordered - c/c++ library headers, system headers, external library headers, internal library headers, project headers - in the files where the inline diagnostics marks the boost include as an error, this is just the first include after the c/c++ library headers. It looks like there is an indexdb file created for each project, however i get these files for only 5 of the 12 projects, no matter how many files of the projects with a missing indexdb file i open, it doesn't get created. And the files where the diagnostics complains about the boost headers are part of projects for which this indexdb file is missing.
I checked the CodeBlocks debug console and recognized a pattern, clang is complaining on a number of c/c++ library heades from gcc, from the names i assume they contain compiler intrinsics. I don't know if its a big help if i post some of these messages or the whole log, but because this is a real project corporate rules require that i remove some information like paths and names from the logs which is quite some work i'd like to save.