Just a question for you on this. I am not sure I am following what is happening here.
You are storing you boot config on an external USB on the router correct?
I wonder if it has something to do with the MIB it is using to pull the startup-config being set to look at flash instead of usb?
You could always check out Cisco IOS MIB Locator</title><SCRIPT LANGUAGE=JavaScript SRC='/ITDIT/MIBS/javascript/mibs.js'></SCRIPT><!-- // BOTTOM HEADER TEMPLATE --><title>MIB Locator - Cisco Systems to see if helps out any.