which game do you talk about? I guess the reason could been the game does not support other than DF0: drive and then discswap dont work? And also some intro disc is separated and not ask for the next disc when its is finished?
In both cases there need some manual swap, which might not been supported by the loader. I guess its could been do the job by two keys (one to shift the disc in left order, and other with right order, which can make sence with games with more than 2 discs).
Howover here its property better to use the WHDloader, not the gamebase loader. Here its allready installed on a harddrive and then there is no such of diskswap issues.