There is a Status War going on in the world.
People who have become religious later in life (either as baalei teshuva or converts) are having a very difficult time proving that they are, in fact, Jewish. Personally, as painful as the conversion process can be, I think the baalei teshuva have it worse.
Thanks to the Holocaust and the USSR, generations of Jewish documentation ceased to exist. Yet despite how widespread this loss of documents was, the Jewish community doesn't seem to have come to any consensus on how these people can prove that their family was Jewish within the acceptable generational time limits. (I believe it's 2 generations? Maybe 3? My understanding is that, as a general rule, if your maternal grandmother was "actually" Jewish, you are still Jewish.)
These problems seem like they should be so common that we would have an answer to them by now. Or at least a standard practice. Unfortunately, it doesn't seem to have happened. And BTs, like converts, get stuck in the middle of Jewish politics that decide who is Jewish and who isn't.
Of course, the opposing argument is that no one would be happy with any standardized procedure for either BTs or converts.