If you try and assign more than 85% (or so) of your available memory to Program Memory then it will default back to a more conservative setting. The OS tries to keep at least a meg or two of storage memory free.
It takes so long to load because the pak file is compressed (gzipped so it is pak0.pak.gz). If you have room on your Storage Card, then you can use DEXplor (registered version) to decompress the file on your Pocket PC. It will load MUCH, MUCH faster with the pak file decompressed. You can also use WinZip on your PC to decompress the file then move it over.
Dan East