Basically, Wii/GC graphics chip has some options which, when switched, make major changes regarding whatever the chip is doing. A lot of games set these options once, and a greater lot sticks to a limited set of configurations (say, dozen) for the entire operation time, so Dolphin developers decided to make a shader for each such config. (Given PC shader limitations at the time, this was probably the only way to take advantage of a typical PC GPU.)
However a little bunch of (typically better) games uses those graphics chip's options very liberally instead and the preparing a new shader for each set of them gets jittery. So some people prefer a rather weird fork of Dolphin that will try to find a matching existing shader instead of waiting for the new one to get ready. An alternative that's apparently in progress in the main project is making one huge shader dealing with all the options; this will probably be way more taxing on the GPU.
