The Nexus 7000 platform stores the startup configuration in some sort of binary or compiled state, not a flat ascii file like you'd find on an IOS device. I think that when you 'copy running-config startup-config' on the Nexus, your running config gets nvgened, compiled and written, rather than just nvgened and written as would happen on IOS.
Frustratingly, you can't copy to the startup-config from any source other than running-config:
N7K# copy bootflash:my-config startup-config This command is deprecated. To obtain the same results, please use the sequence 'write erase' + 'reload' + 'copy
running-config' + 'copy running-config startup-config'.
There is some documentation which indicates otherwise, but it's been updated. The only supported way to load a fresh configuration on a Nexus 7000 is the one recommended in the error message above.
Thank goodness for terminal servers.