Similarly with pIgh. Even in English we seem to never talk about a singular "ruin". For both, even though the English translation appears in plural, the words are treated as singular in Klingon.
However, I'm sure mike-lima was questioning the conjugation of the English verb, not questioning the plurality or verb prefix in the Klingon sentence. And I have to admit, though I'm a native English speaker who has studied many other languages, I'm not certain which conjugation is correct here. I would say, "what inhabits the ruins," but "energy beings inhabit the ruins." When we use the phrase "what seems to be energy beings" I'm not completely sure which influences the conjugation. I lean towards the verb conjugating for the plural subject and have changed the "best" translation to "inhabit" (and the translation shown at the title of this sentence discussion may change to reflect that).
I'm also not completely certain whether it should be "seem" or "seems", but this time lean towards "what" acting like a singular subject to make it "seems".
I would definitely say "What seem to be energy beings inhabit the ruins", and find "What seems to be energy beings inhabit the ruins" totally ungrammatical. I'm basing that only on my own spontaneous reaction as a native speaker of English, though; I've been unable to track down any discussion of the matter. But if the fused relative "what" is triggering plural agreement with "inhabit", it seems reasonable that it would do the same with "seem". And if "what" always took singular agreement, nobody would ever say e.g. "what seem to be", but Google reports hundreds of thousands of matches for it.
I don't think we're going to find total agreement on any of the possabilities, even if we did a poll of native speakers. I would guess that a majority of speakers would find the singular "what" determining the conjugation of "seems" and the plural "beings" determining the conjugation of "inhabit". I can certainly see your argument for agreement between the verbs and all the variations are listed as accepted translations (even seem/inhabits, for good measure).