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The Program Files folder is situated on the main memory of the Pocket PC which as you know, is limited to 64Mb. The OS uses this memory for everyday things so its advisable to avoid installing programs there if you can get away with it. (Some, especially today plugins, must be installed into the RAM).
The BIS, on the otherhand is flash memory built in to the pocket pc and much more preferable to use for programs. Installing programs here doesn't affect the main memory of your device. The more main memory you have free, the more can be used for running programs.
The BIS, the Secure Digital card slot and the Compact Card slot all are independant of main memory and should be your first choice for installing programs, storing documents, etc. i.e. BIS, SD, CF are all equivalent to a hard drive on a PC whilst the main memory is the RAM.
Another detail: BIS is slower than SD or CF to write to but not that much slower to read from - ideal for programs, not so for documents, mp3, etc.
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