Hmm, this is still quite puzzling, and curious...
Clearly this is not a general problem with Alembics, or we would all know a great deal more about it. The other thing that confuses me is this: if the strings are of a strong enough material to wear grooves in the saddles, then it simply doesn't makes sense that those grooves would in turn be strong enough to break the strings.
Even more to the point, the object of the saddle is to keep the string from moving at that point, so if the saddle is fitted properly to the string, then the wear should not be caused by movement... and there isn't enough pressure involved here for strings to just sink into the brass or other materials.
I don't question the fact that you've had a (fairly unique) problem, but there still isn't enough information here for me to make any sense of it. I'm still wondering if you have an extreme break angle or something, but that's about the only theory that makes even a little bit of sense to me.
-Bob