I am not seeing any issues with this in the latest version, it has the same fix and it works correctly for me. If I have 2 feed managers with different feeds then the outbound aggregated feed of each Feed Manager instance has the correct content.
The lates version is 2.3.1.5.
Important. Your current version 2.2.5.8 is very old, it only required ASP.NET 2.0. To upgrade to the newest version you need ASP.NET 3.5 SP1
You will also need to be aware that any custom skins you have will need to be modified to work correctly with the new versions of mojoPortal. See http://www.mojoportal.com/important-skin-changes.aspx
Hope it helps,
Joe