HighGfx is picky about what monitor you use it with. It's really pushing the system to it's limits. Try some of the other modes, like 800x600x16-color SuperPlus, I've found that worked on every monitor and TV I threw at it. At it's most basic, the Indi ECS is just a scan doubler. Do other modes display correctly at 31KHz? NTSC 640x400, 320x200, etc.?
Also make sure your firmware is on 1.10 (not 1.01) for the more advanced screenmodes. You may need to tinker with the config tool, but the "out of the box" config should work fine with most normal Amiga screenmodes and modern displays.