The Wii/GC stuff (though I am not sure about
Nintendont) is usually that if it tries to read from the GBA cart's Flash or EEPROM save memory that was in the retail game and can not find it (all GBA carts use SRAM type save memory, that is what patching the games changes and why they batteries when original carts might not). Assuming it is not also
Nintendont having an issue then you tend to have to hack the GC game, and to the best of my knowledge nobody has bothered to do this for any GC game -- it was done for the pokemon pal stuff on the DS and that is about it.
The GBA-GBA stuff is usually more people using bad cables (though that is probably not the case here) or the patching troubling the timings of the games. We occasionally see similar things with other GBA flash carts. The solution there seems to be disable as many patches as you can (especially sleep and soft reset) or even try disabling all patches but if you need one to help the game save then try
http://ezflash.sosuke.com/viewtopic.php?f=12&t=17714
You will need a method of getting the GBA game over to the 3 in 1 without anything being changed on it, I am not sure what the various cart management tools have the option for these days, though you might be able to get away with one of the older tools.