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I'm certainly no iSeries guru but I did come across this
IBM APAR #II14247 (contains technical details for System i Access for Windows on Windows Vista).
You'll want to visit and read the page but here's an excerpt:
APAR#: II14247
Component: INFOAS400 - AS/400 Information
Release(s): R540, R610
Abstract
SYSTEM I ACCESS SUPPORT FOR WINDOWS VISTA - TECHNICAL DETAILS
PART 1 OF 3
Error Description
** Last updated March 24, 2008 **
SYSTEM I ACCESS FOR WINDOWS AND WINDOWS FIREWALL
================================================
In Windows Vista, Windows Firewall is on by default, and is
configured to block incoming connection attempts. The following
applications within System i Access for Windows may use TCP/IP
communications internally to get their jobs done, and Windows
Vista may show an alert when they initiate such communications:
- System i Navigator (uses "cwbunnav.exe" and "Java Launcher")
File(s) that may need unblocking:
(System i Access for Windows install path)\cwbunnav.exe
cwbunnav.exe, iSeries Navigator, V5R3, AS/400 errors
On a Windows XP Pro, and iSeries Client V5R3 with service pack SI28055. Navigator comes up with cwbunnav.exe error. Have installed this same version on several other Win XP Pro desktops/laptops with no problem. 
