anyway since you've reinstalled it then its been done but for future some pointers:

No,NiTDroid doesn't interfere with your flashing process...

Also when the logo with the usb icon comes up wait 5-7 secs for flashing to start...just make sure your usb connection to the phone doesn't get loose hence causing a normal boot-up instead...its quite sensitive to loose connections so always keep it on a hard place...