New versions of MsgFiler Engine 1.1.9 and the Original MsgFiler Mail Plugin 2.2.4 have been released. These bring support for OS X 10.9.3, which was released earlier today.
It is common for OS X updates to disable your Mail plugins. To get back fast-filing performance with MsgFiler 3, simply:
- Download the latest version of the plugin.
- Decompress the ZIP archive.
- Double-click on the disk image file.
- Go to the Finder.
- Hold the option-key down and click on the Go menu.
- Choose Library.
- Navigate to the
~/Library/Mail/Bundlesfolder. - Drag the
MsgFilerEngine.mailbundleorMsgFilerPlugIn.mailbundlefolder into the Bundles folder. - Quit and relaunch Mail.
Verify that the plugin is active by clicking on the Message menu:
- MsgFiler Engine: A menu item labelled “MsgFiler Engine 1.1.9” will appear at the bottom of the Message menu.
- Original MsgFiler Mail Plugin: A menu item labelled “Move with MsgFiler” will appear at the bottom of the Message menu.
MsgFiler 
Constantly getting an error when starting mail..
“Mail has disabled the following plug-ins:
MsgFiler Engine
Contact the makers of these plugins…
I’ve placed both MsgFilerPlugin.mailbundle & MsgFilerEngine.mailbunder in ~/Library/Mail/Bundles.
Resolved by placing the MsgFilerEngine.mailbundle in /Library/Mail/Bundles (not within my home directory)
Sometimes this happens with certain OS X configurations. The preferred method is to place it in your user library’s mail/bundles folder, but if that fails, try Jacob’s tip.