Doruk,
This is a pretty strange issue, we haven't seen this before. Try importing and building a different project from Resource Explorer and let me know what happens. Also in CCS, on the main menu bar, click Windows-> Preferences and under the C/C++ tab, select Build->Build Variables and send me a screen shot. Make sure that show system variables in checked. Here's mine,
If I can't spot any issue from this, I'll message you directly for the Webex. That way, we can share screens and I can see if there's anything off in your setup
Moses