According to the SDK all the *.addin files from the all users and current user folders are lumped together and then loaded in in alphabetical order. The individual command/applications within each *.addin file are loaded in the order they appear in that file.
So depending how you create your *.addin files (either one per command or one file with all of your commands) there are two ways to control the order; either rename the *.addin file so that it appears in the correct order alphabetically or move the individual <AddIn>...</AddIn> groups into the order you desire.
