Pretty much all "media player software" programs that I have used, perform an auto-import when you first open the program. eg: iTunes, WMP, WMC, Zoom Player, etc. Strange that MC waits for two hours??
That is what happens when a new installation of MC is first started, after a 45 second countdown, and a lot of people hate it.
A lot is happening when MC is first opened. Not only in starting the software, but usually, for most people, when they start MC they want to start watching programs, and don't want their HTPC slowed by background processes. Not that Auto-Import would actually slow MC much, usually.
Anyway, you are using a hybrid implementation of WMC and MC, so you should expect a few little quirks. As Brian suggests, if you leave MC's Media Server running, all the files will be there waiting for you. That is the intended way to use MC, I believe.