When you run copy run start, do you get any indication that the operation did not complete? Can you change something in the config, like adding a description to an interface, and then run the copy run start again to verify that is is completing? Manually look at 'show start' and then 'show run' to verify that the config was saved.
If you still see the problem with show run diff after these steps, and you can confirm that the config is being saved with no problem, let us know and we can dig deeper.
We are having the same problem. It is throwing off our configuration management tool. This is happening for all of our MDS switches and appears to be related to certain commands not being present in the startup-config.
For example port-channel configurations:
interface port-channel 1 + no shutdown
interface port-channel 2 + no shutdown
interface port-channel 5 + no shutdown
The no shutdown appears in the running-configuration but not in the startup-configuration.
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