I don’t think there’s any grammar rule in English that requires the dependent or subordinate clause to be also in the past tense when the independent or main clause is in the past tense; that would make English an impossibly restrictive language for describing with events as they happen in time. You are perhaps referring by mistake to the so-called
normal sequence-of-tenses rule for reported speech or indirect speech. Reported speech is, of course, the kind of sentence someone makes when he or she reports what someone else has said. And under the normal sequence-of-tenses rule, when an utterance takes the form of reported speech and the reporting verb is in the past tense, the operative verb of that utterance generally takes one step back from the present into the past: the present becomes past, the past usually stays in the past, the present perfect becomes past perfect, and the future becomes future conditional. (Click this link to my forum posting on
“The proper way to construct sentences for reported speech”)
Nevertheless, let’s see if it’s correct to use the past perfect for the verb phrases in the “that”-clause of the sentence in question, as you have done: “Not until I requested for my GSIS claim this March did I find out that my service record
had not been closed yet because your office
had not received the endorsement letter.”
In that sentence, the operative verb of the dependent clause is “requested” and that of the main clause is “did I find out,” both of which are in the past tense. We must keep in mind, though, that they are both in the past tense not because there’s a grammar rule requiring them to be always so together, but only because it just so happens that it’s what the particular situation requires. As to the verb phrases in the “that”-clause of the main clause, namely the verb phrases “has not been closed yet” and “has not received,” there is actually no rule whatsoever that requires them to have the same tense as the operative verb of the main clause. This being the case, the tense they will take will not be automatically the past tense but will be dependent only on the sense of the situation being described. In this particular case, they have to be in the present perfect because at the time the letter was written, the two conditions described—“has not been closed yet” and “has not received”—are still subsisting; in fact, they are the very basis and justification for the letter-writer’s request.
The past perfect would apply to those two conditions if they are no longer subsisting. Indeed, only in that event can we use the past perfect for those verb phrases, as you have done in this rewrite: “Not until I requested for my GSIS claim this March did I find out that my service record
had not been closed yet because your office
had not received the endorsement letter.” But the use of the past perfect here would wrongly imply that after the letter-writer discovered the problem, that office thereafter received the endorsement letter and duly closed his service record. This isn’t the case at all, though. Those two conditions are still subsisting up to the time of writing, so it’s logical for the letter-writer to use the present perfect tense for those two verb phrases: “Not until I requested for my GSIS claim this March did I find out that my service record
has not been closed yet because your office
has not received the endorsement letter.”
I hope I have adequately clarified the tense usage for that sentence.