Right now i have commented out new and delete operators and all is working fine. I've tried to investigate remained errors reported by valgrind, but they seems wrongly detected (except memory leaks maybe), at least i can't say what is wrong with code looking at reported place. Many errors of wrong reading type are related to CPU optimization in libc, when code reads strings by 8-bytes (64 bits) blocks, but i believe it's safely processed.
I can say that all that memory allocation related to crash where done in video part (crashes in X11 libs, X.org libs, radeon driver, SDL etc.) Roughly two months ago all was fine, so i guess this is related to some optimization in video drivers (in system or game). There are two possible causes of crash - wrong function used to free memory (our delete in place of original, when memory was allocated by original new) and attempt to free memory already freed in Mem_Shutdown. First seems more real (at least i have read about such thing in TCMALLOC docs and there are complains about memory sentinels which is absent in original new), second can be case too - it's bad idea to free all allocated memory at once without notifying owners (they can try to use it or free). Of course we can be sure that our code is not using freed memory, but we can't say that about external libs of they are using our operator new.
I'm looking for good IDE to work with code. Something better then just editor with syntax highlighting. I have tried Eclipse (don't understand that thing) and Codeblocks (crashes on opening game project). Now looking with Anjuta but it lacks some features.