You have to use XBPartitioner 1.1 or later to format partitions over 256GB or you'll get data corruption. That's almost certainly why your F partition is disappearing. You should always check the cluster size after formatting - see the link in my signature (Format hard drive / check cluster size) for details.
However, the softmod shouldn't disappear even if the F partition does become corrupt. Unfortunately you neglected to mention which softmod you installed and with which options, where you install XBMC, how you launch it (direct dash replacement or shortcut), or the symptoms when the softmod disappears (LED colour, screen message, will it run a game, will it run a rescue disc), so it's difficult to provide any firm advice.
Fix the cluster size first, then if the softmod problem persists post back with the information I suggested and we can take it from there.
This post has been edited by Heimdall: Jul 11 2012, 10:32 AM