This is one reason I dislike "passive" Perception and Insight allowing players to "take a 10" with no constraints. All other skills in 4e require that the PCs take several minutes to "take a 10", but these don't. With that, one good way to break this a bit would be to have the PCs under stress. There is something preventing Holmes here from really focusing, so even his passive skills can't pick up on something. Might help a bit. This is just passive Perception too, which at least in my games, equals out to "you know something is here, now make a specific check".
Also, I find it weird that the replacement with Arcana isn't limited to "once per encounter", like Arcane Mutterings, which is something I've abused in a campaign before. That is certainly something I would refute with my player and discuss. If the source of the issue comes from a power, how is he using it as his passive check? Why does he have it for later checks in the same "encounter"? Again, going back to passive perception simply being savvy enough to know that something is off, but having to make a dedicated check to find it.
That just doesn't flow. Once the source of the replacement gets sorted, you can really start solving this problem. If Sorcerous Eyes is causing an issue, remember it's a limited power, so require an active roll instead of just allowing the PC to take a ten on it/use it as his passive check. Once you are past that, have him declare to be looking for specific things with his super Perception, not just auto scanning the room and seeing everything. This will actually force player to think about what he is doing and make follow up rolls. I'm guessing he's basing this on "Sherlock", which if you notice doesn't sweep the room and get everything on the first go, he often is following up on his first (or passive) insights. That too will help to burn up uses and give the rest of the party a chance to shine, since they will need to help him once he's burned his limited super perception/arcana replacement power.