|Problems? Is your data what you think it is?|
An off-the-wall guess that I have no way to verify. Could it be that you are running out of memory? A quick browse of Mail::Box and it's associated modules leads me to believe that they form a quite heavily nested hierarchy of modules with each level adding another hash or two for each item. Large volumes of nested hashes, even when each individual leaf hash is quite small, can rapidly consume large volumes of space.
On my system, Perl sometimes dies silently when it runs out of space.
Maybe you could monitor programs memory usage when running it on this large directory?
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
Lingua non convalesco, consenesco et abolesco. -- Rule 1 has a caveat! -- Who broke the cabal?
"Science is about questioning the status quo. Questioning authority".
The "good enough" maybe good enough for the now, and perfection maybe unobtainable, but that should not preclude us from striving for perfection, when time, circumstance or desire allow.