Programming Arduino from Eclipse: Compiler Issue

Hello, I've been trying to figure out how to use other IDE's to program ARduino. I researched trying to use Visual Studio, but it's impossible to change the MSVC compiler used to compile C++/C files. You can't really change the tool chain in Visual Studio unless you use make files which I don't have experience in and become hairy pretty quickly.

So I decided to follow this post http://playground.arduino.cc/code/eclipse and configure eclipse. Everything went well and I'm able to build the core and applications based on those core, but just realized that the avr-g++ and avr-gcc compilers used to compile the C++/C files are coming from the installation of WinAVR (C:\WinAVR-20100110\bin), not from the ARduino install (C:\Arduino\hardware\tools\avr\bin), even though I have set the AVR GCC paths in Preferences->AVR->Path as suggested in the post.

I verified the wrong compiler is being used by renaming the compiler exe in the ARduino directory. No error was produced, indicating that compiler wasn't being used. However when I rename the compiler exe in the WINAVR directory, compilation fails. Has anyone else encountered this?