this is i think to be expected, as far as I could tell, eclipse will only import the files, things like include directories, and also things like chibios will not be setup, nor with the compiler flags/defines etc.
what this means, is you need to use the make and the makefile to compile, you don't compile directly from eclipse...
UNLESS you plan to do all the above manually, and then you will have to be very careful that you see aLL the defines and flags correctly, otherwise it will compile not but run as expected, frankly i didn't think it worth it, as you can still debug without this.
(or of course, if you can find a way to get eclipse to be more intelligent about parsing the makefile, to bring in all settings/includes/defines/compiler & linker flags. which I couldn't ... but I'm not a big eclipse user)
another point, last time I tried, patches could not be debugged, as the symbol references were not aligned correctly. it was a while ago and I didn't look too deeply, but it did not 'just work'... id be interested if you have more success in this.