This is something you may run into, especially if you're running Integration Services on a machine with multiple instances and at least one of them is a SQL 2K instance.
The Integration Services server does not support instances, but is aware of SQL Server instances and can be configured to reference a particular instance. Here's how.
There is a file called MsDtsSrvr.ini.xml in the %PROGRAM FILES%\Microsoft SQL Server\90\DTS\Binn folder. If you open that file you'll see something like this:
There are a few interesting settings here, but this one determines which server the IS server will reference for enumerating packages in MSDB:.\YUKONB3
This tells the server to reference the local server instance named "YUKONB3". It can just as well be something like:
. or (local) or MYSERVERNAME etc.
If you make a change to this configuration file, make sure you restart the service in SQL Server Configuration Manager or the services control panel app.
Hope this helps,
Universe.Earth.Software.Microsoft.SQLServer.IS.KirkHaselden