If you run the following query at the msdb database (one of the system databases) at your SQL Server, do you get any results?
SQL Server 2005:
SELECT [folderid]
,[parentfolderid]
,[foldername]
FROM [msdb].[dbo].[sysdtspackagefolders90]
SQL Server 2008:
SELECT [folderid]
,[parentfolderid]
,[foldername]
FROM [msdb].[dbo].[sysssispackagefolders]
This table lists all the folders that should be displayed in the MSDB folder. There is an analogue table for the packages.
If you create a job in SQL Server Agent and you create a 'SQL Server Integration Services Package' step, do you see your folders/packages when you click on the browse button by Package?
(or similar, if you create an Execute Package Task in SSIS, can you browse to your packages?)