The reason is due to drivers. Linux has the driver support for your Win98 FAT partitions and can therefore see them fine, but Windows doesn't have drivers for Linux partitions that are formatted with ReiserFS, Ext2/3, XFS, etc. Drivers do exist, however, that you can install in Windows that will enable you to use/view your Linux partitions. Some examples are:
, and Ex2ifs
Hope that helps!