Here is my setup. I have the latest BootMii beta5 and I believe I have System Menu 4.1 (if not 4.0; I can confirm if this information is relevant) and I have BootMii installed on boot2. I have two SD cards which I use for my Wii, a 4GB card (which is incompatible with BootMii) and a 2GB card (which is compatible with BootMii). If I need to boot into BootMii from startup, I'll put in the compatible 2GB card and it works great; BootMii loads right now. But normally, I have my 4GB card always inserted as it has all my Homebrew Channel apps on it...
Here is my issue. When I power on my Wii with the 4GB card in, it will sometimes (50% of the time) flash the slot quickly twice (as BootMii expects) but it will not present me with the warning "Press A" black screen... The Wiimote actually loses Bluetooth connectivity as well. The only thing I can do is hold the power button down and restart the process... Usually the second try, it will boot to the warning screen and I can press A just fine.
I tested it out to see if booting without the 4GB incompatible SD card in the slot if it would work... 5 out of 5 times, it booted just fine.
Before I upgraded to BootMii beta5, I was at beta4 and noticed this issue as well... But I believe I was able to resolve it. What I did was removed the IOS BootMii files from my 4GB incompatible card (essentially deleted the 'bootmii' directory) and this seemed to fix this issue... I tried the same thing with beta5 but it does not work... It seems to look to the incompatible SD card to boot from boot2 and just hangs instead of bypassing it... Does anyone else notice the hangs if their card is incompatible and you have BootMii on boot2?