http://blogs.msdn.com/windowsmobile/archive/2006/06/07/621132.aspx

Everyone that has a device (let it be an iPAQ hx or a Dell Axim x50(v)) upgraded to WM5 knows what problems the compaction service (filesys.exe) causes. The problem has been addressed by Pocket PC gurus/hackers (including me) several times, with varying success. (See for example this article.) Now, well-known Windows Mobile Team blogger Mike Calligaro addressed this problem in his blog, with particular attention to the WM5-upgraded HP iPAQ hx4700. The article is a nice read to anyone that wants to know more about the compaction process. Also, it points the reader to the new, free, much more WM5-friendly (it doesn't write temporary files back to the main storage) DockWare version, which is highly recommended for all hx4700 users (go and get it!). Unfortunately, there are no solutions/hacks provided in the article. However, it still contains some good news: they've sent device manufacturer OEM's the way of speeding up the process. Now, we're in the hand of the manufacturers: hope they do issue some kind of an update. Unfortunately, these hacks can not be implemented by hand (on, for example, the Registry level). With some laborous ROM reverse engineering, recompiling/hexediting and re-flashing the entire device ROM, this can be done, even if HP/Dell don't bother releasing a new ROM version, though. Any Pocket PC guru having the necessary time to do it? ;)