First, the semi-colon should be a comma. or, probably better, the description of the blackboards and chemicals should be broken into two separate sentences. Aside from that, I don't see a punctuation problem. But there's a lot of confusing and/or meaningless verbiage:
"Theodore shoved them through a maroon-colored door". So he broke down the door by shoving them through it? Or did he just open the door and push them inside? (I'm assuming you're talking of other people, but that's a context matter). "Maroon-colored". What, other than colored, could you mean by "maroon"? What does the color of the door matter, in these circumstances? For that matter, why even mention the door, unless there's some story reason to do so. Whenever you go into another room, you generally do it via a door. Now, if he transported them into the room through the wall, that would be worth describing.
In the second sentence, the whole business about "in one corner (if round rooms could have corners)" just doesn't work for the most obvious of reasons: round rooms don't have corners. The focus of the sentence is on the blackboards, and the description of those could be greatly simplified: Inside were blackboards chalked with insanely-complicated mathematics.. "Smeared" doesn't seem quite the right verb, because that implies, well, smeared, rather than readable.
They just entered the room to be confronted with all this stuff. Evidently no one else is present in the room. How is the room lit? Did they have to turn on lights, or did they carry their own? How do they know the bottles and jars are filled with chemicals?
I'd lose the entire "that were soon to serve some purpose" phrase. It's superfluous. They wouldn't be there if they didn't have an intended purpose. As for "designs and drawings of half-built gadgets", nobody designs a half-built gadget. If there are no actual gadgets, nothing has been built. And you're not going to recognize these as drawings and designs right away. All you'll see up front is papers spread out on the tables. You have to make a closer examination to determine what's on them.
And there are a lot of "weres". None of those are used incorrectly, but a bit of verb variation would be helpful, and there are simple replacements, like "stood" to describe the blackboards.
In short, you're trying to cram way too much detail into this paragraph, and it loses it's intended meaning under the weight and confusion of the presentation. That's why you feel there's a punctuation problem, I suspect.
Try this: Become Theodore, act out the entering of the room, and the discovery of these strange, surprising objects. What do you see first? What do you discover by closer examination? How do you discover things, like the jars holding chemicals? The nature of the drawings?
In exploring a strange room like this, these characters are going to use some deliberation to figure things out. Render that process in your narration. Don't hurry. Don't try to cram everything into a dense knot of turgid sentences. Periods are not precious. The universe contains an unlimited supply of them.
caw