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There are some programs that do not like being on a storage card. Some won't actually go there, even though you tell them to and they make a folder. (look through your program folders on the flash card sometime and see if some aren't empty). The general idea is that flash card drivers need to load during startup, i.e. soft reset. If you have programs that need to load support files, or are startup apps themselves, like today screen apps, SIPS, etc. The flash card drivers may not be ready when the program tries to load.
Your situation may dictate what you put on the flash card as well. If you only have one slot, and you change out your flash card, with one having music and the other having programs, probably putting your favorite media player on the programs flash card isn't a good idea.
Think of the PPC more like a PC. You generally can't install a PC program and then just drag the program folder from one place to another and expect the program to function. PPC is the same. There are of course programs on both platforms that are standalone executables that you can stick and run from anywhere.
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