One thing I noticed, Christian, was that there was a certain amount of info-dump in the form of things that Vulgaris would not be likely to notice or think about while he is running away. The pictures on the walls, for instance. Writing in a close third person viewpoint (which you are, as soon as you directly quote someone's thoughts), you have to keep asking yourself as you write whether the things you mention would enter your POV character's mind at all during that particular moment.
I think these things also slow things down and detract from any sense of urgency, which I believe is the most important thing you should be trying to convey as the boy is running in fear of pursuit. Which brings up another problem. Had Vulgaris simply jumped to his feet, bowed (or whatever gesture of respect would be necessary in that situation) and walked off, the Liberatos would probably assume that the boy has simply been sent on some errand. He would either ignore Vulgaris, or ask what he is doing. But the boy leaps to his feet and runs. If anything would inspire suspicion and pursuit, that would be it, but the Liberatos does nothing. To me, this doesn't really make sense. You have, apparently, written this scene with Vulgaris running because that is dramatic, but his reason for doing so (and the lack of pursuit) strike me as so implausible, that his encounter with the Liberatos and his subsequent flight seem to be tacked on for the purpose of creating drama, rather than anything intrinsic to the scene or situation.
There is also the matter of the candles. Back in the days when people used candles as one of their principle sources of indoor lighting, they were expensive, they were carefully doled out and those of the lower orders who had them used them very economically. Servants received a very meager ration of burned down candle stubs as part of their wages, and the number they received was directly related to their importance in the household, and they would use those stubs only at need -- perhaps to climb the stairs in the dark and find the way to whatever tiny room or garret they slept in. If they were fairly important servants and their ration of candles was sufficient, they might light a candle before dressing or undressing (and then blow it out immediately). Someone as humble as the boot boy would be lucky to get any. Vulgaris, of course, would know the value of candles, and he would know that he could not possibly use up several without the owner of the candles noticing. This would be, in a very real sense, theft. There would be an investigation, and dire consequences if he was caught. This would surely be in his mind as he takes the candles out of the chest, and he would do so with considerably trepidation ... if he would do so at all.
In addition, his interaction with Equilibrium would involve not only the question of what he has seen or learned that he shouldn't know, but the theft of the candles. It is highly questionable that Equilibrium would wish to take on a thief as his assistant, and moreover a thief who has just robbed him.
The scene would be more realistic, I think, and be a good demonstration of how thirsty Vulgaris is for knowledge, if he came in with a pocketful of his own carefully hoarded candle ends, which he had saved by going a month or so feeling his way to his bed in the dark. That would also explain the question of "Why today." Today he might feel that he has enough bits of candle to make a trip to the room with the books worthwhile. Of course, that removes the explanation for opening the chest, which is a problem, but you might think up another reason for him to do so.
It seems very odd -- whether because of the candles or anything more important the chest might contain -- that Equilibrium would leave it unlocked in any case. Perhaps, though, such an odd oversight might be the very thing that inspires Vulgaris to open the lid. If there is a lock but it is obviously not fastened that might be an irresistible temptation to the boy's curiosity.
