I'm going to assume that you know what you're talking about when you say that it's a single DNS server. I'm skeptical because you have not shared your methodology for determining this, but my answer will take it as a given that this information is accurate.
Normally you would perform a query, look at the observed TTL, and query again once that TTL expires. You would continue this until your predetermined sampling period is reached and compare good answers against bad answers.
Unfortunately, the operative word here is "normally". You're looking for a deterministic answer, but these are hard to come by once a server is compromised and in most cases you have to throw logic out the window until you know the specifics of the exploit methodology.
- Given your other question on security.SE, it's more likely that the server software itself has been compromised than this being the result of being bombed with forged answers.
- Bombing of spoofed packets would always cycle out on a TTL, but other methods
might change the reply unpredictably before the TTL window has
expired. In the latter case, it's hard to tell whether the change is
due to a refresh or not unless you're 100% certain that you're
dealing with a single server and not a farm behind a VIP. TTL will vary pretty consistently in the latter case.
Long story short, you're putting in a lot of work for a problem that isn't yours to own, and since you don't own it you have very few ways of making sure that your gathered information provides a useful conclusion. (aside from an academic exercise in ratio of raw good:bad replies over time, which would turn this Q&A into one of those "gimme the codez" questions that we frown on on this SE site)