When you extend Esri's ArcMap with both an Extension, a Toolbar and a number of Commands, is the order in which these categories are loaded by ArcMap well-defined? (I.e. are Commands always loaded before Toolbars, Extension always loaded before Commands, etc.)
I'd recommend reading the "About extensions" topic in Extending ArcObjects | ESRI Developer Network (Wayback Machine link) which covers just-in-time extension loading. Ideally all extensions should be JIT extensions. Tools and commands can control the startup of a JIT extension etc.