My experience is that after a period of real internet problems (ISP is down but not at the first hop, or real latency is high), when the real problem is fixed, then apinger get too optimistic, reporting latency that is too good to be true. I guess something in its rolling averaging algorithm goes wrong after it has had big values and then gets much smaller ones come in.
Anyway, for me it usually stabilizes back to a believable value after 5 minutes.
Yes, the code has got too complicated trying to patch it to handle all sorts of things that can happen on-the-fly as interface events happen and outstanding IOs die and… Maybe it can be fixed by just 1 more patch?!
Realistically, as others have commented elsewhere, it is time to make some requirements and write a multi-WAN multi-target monitoring program from scratch.