You might be able to stop that message by removing the stale.txt file from the map using VIDE later on.
For anyone who's interested in learning more about what's possible with VBSP arguments, check out the page for VBSP on the Source SDK wiki. For example, there's an argument that lets you compile entities, lighting and so on in to a map that has already got packed stuff inside it so you don't need to go through the whole packing process again later on. Probably even uses the same cubemaps, too.