I have two NOT codecompletion related issues =)
They rank about the custom compilation commands defined via the advanced compiler options.
I've setup a command that transforms html files to header files to include them as a resource. The first problem is that these files are always "compiled", although I modified the program that does the conversion to equalize the timestamps (ie the output has the same modification time as the source). The second problem is that IF they need recompilation, depending cpp files don't get recompiled in the same run, so basically CB doesn't reevaluate dependencies when compilation runs. I see that this is a vaild optimization, but for custom commands it's an error source. CB should recognize that a command creates c/h/cpp/hpp files (or more generally "files that are sources for other compilation commands") and reevaluate compilation necessity after they are "compiled" or, as an alternative, have a switch for custom commands that says "reevaluate dependencies after running this".
That problem also influences compilation order, but that can be fixed by assigning priorities.