No, Bob didn't say that LC now matched the power flows in the real Chicago, so the problem was solved; he said that LC had a power flow set up the wrong way the last time he looked at the model, but that now, when he was looking at it, the power flow was correct. One scenario involves the real world changing but the model staying the same, while the other involves the world staying the same and model changing between one viewing and the next. If the real world had changed, Bob and Harry wouldn't have had any need to go through the part of the discussion in which they talked about how someone would've needed to get past the wards, examine Little Chicago, and realize how to fix the problem. Bob would have known the difference and we would've had an entirely different mystery to think about.
Proven Guilty, page 471, paperback:
"I found something wrong with Little Chicago's design." I swallowed. "Oh. Wow. Bad?" "Extremely. We missed a transition coupling in the power flow. The stored energy was all going to the same spot." "That's ... like a surge of electricity going through a circuit breaker, right? Or a fuse box." "Exactly like that," Bob said. "Except that you were the fuse. That much energy in one spot will blow your head off your shoulders." "But it didn't." I said. "But it didn't," Bob agreed. "How is that possible?" "It isn't," he said. "Someone fixed it." "What? Are you sure?" "It didn't fix itself," Bob said. "When I looked at it a few nights ago, the flawed section was in plain sight, even if I didn't recognize it at the time. When I looked at it again tonight, it was different. Someone changed it." "In my lab? Under my house? Which is behind my wards? That's impossible." "No it isn't," Bob said. "Just really, really, really, really, really, really difficult. And unlikely."
The issue that I'm taking with Bob's statement is that he never stated where the transition coupling was at on LC. Kind of odd, considering that he's the one who brought up the conversation. Altering the power flow out in the real world so as not to have Dresden blow his head off his shoulders, even if it was only a momentary alteration, would have been much easier as opposed to someone going into Harry's subbasement. And Bob knows that. Bob being locked in Harry's basement doesn't exactly lend itself to his noticing a momentary flux in the power flows around the city, ya know? After all, Bob didn't notice the mishap until a few nights later- even though he saw it
hiding in plain sight the first time he looked at it- so he therefore wouldn't have been looking for any shifts in the power flows around the city to begin with. (Simply put, whomever kept Dresden from going kablooey acted by momentarily taking the circumstance out of the cards, rather than risk a fix in front of Bob.)
On top of that, we have Bob stating that in all likelihood, no one did get into Harry's basement to fix the issue. It was fixed elsewhere first, and in the basement after the trial run.
I've also generally found that the either/or principle applies when we have all the information. We don't know why Bob missed the transitioner, even though he said he could see it.
As for how someone else knew LC was messed up- if they were running their own version, they probably noticed when all those small chinks and nicks appeared in the buildings, roads, etc. and took care to fix the model, lest they end up having to fix a much, much bigger problem.