The RAM loss is caused by the nature of flash RAM.
Flash RAM is allocated in blocks, and unlike static RAM, flash RAM cannot be erased. Instead, if you want to erase a bit in a block of flash RAM, the entire block minus the bit must be copied to another block of flash RAM. Thus, there must always be at least one block of free flash RAM at all times.
The Apple MessagePad actually keeps a few blocks free for performance reasons. These free blocks account for the missing RAM.
This article was published in the "Information Alley": Volume II, Issue 9, Page 19