than standard procedure to get into a CISCO router.
A network to me is all the individual hosts in the network including the routers and switches.
If the term network here is being used to refer to only the router, then they have to only be worrying about the router configuration (odd there is no backup).
I am guessing it is the admin control over the entire system (where system is not one host but the collection of hosts), it has to go deeper than just one or a few routers. If it doesn't then whoo this is day 3.
Physical access is not game over as far as security is concerned, if the systems are running off an encrypted backing store, then that would still need to be defeated, of course they could get the liquidN and try to hotswap the memory :)
And hey San Fran has got the tech community on its doorstep, why haven't the simple solutions worked yet, there has to be some reason.
Their thinking could be, as long as the system is working, then they will just take the more cautious approach of doing nothing, once it requires admin access then they will probably start throwing the solutions at it. That is a possible scenario, but of course they don't know for sure everything is ok apart from the access.
And he is claiming innocence, the access codes given could have been genuine as far as he knew it. And it could just be coincidence, some cybercriminal just hijack'd his account, that could explain the monitoring of the other admins. You are not going to gain too much monitoring your colleagues, much simpler to chat to them, and unlikely they will slag you off in an internal email, they will use the water cooler for that. But, they will email about technical mechanisms in the company, something he probably would have already been privy to but a cracker wouldn't, and a cracker would want that info.
And here is another idea, the password he gave may have only been correct for that time period, therefore the access code was valid for say 5 minutes but not after that.
Something really doesn't stack up here, 3 three days is too long not to have regained control, or at least regained control of key elements to the system.