It was quite funny...
I had discovered that my NTSC MGS: Twin Snake running in 480i, it was strange 'cause I remember that a lot of NTSC games must support 480p mode, so I decided to fix it with NeoGamma R9 Beta 56 options, firstly I had tried NTSC480p mode - nothing, just green screen, then PAL60(480p) - the same dead screen and the same forced Wii reboot.
Also had tried some other options in combination with "Video Patcher" setting etc. and nothing too... Then I just gave up trying, restored all Neogamma options to default, made some search with google and accidentally found out a
"Hold the B button" method, just held B when MGS was loading and that worked, the game itself asked me about Progressive mode so I chose Yes and voila - fully worked game in 480p mode...
So what is current situation with progressive mode and GameCube games?
I know that I may not realize something but for me that situation looks strange and if I hadn't found
"Hold the B button" method I would never get progressive mode...
P.S.
And yep, sorry for noob question