Software which can generate checksum for large, deep directory

[The111]

I have quite a bit of data that I backup on two external drives which I keep at two separate locations. I call it my ghetto RAID, and I'm sure plenty of people would never use such a system, but I do. I don't like relying on backup/synchronization software, so I manually maintain each archive and keep them in sync. However, I like to have a foolproof way to verify each drive is identical (and not corrupted anywhere). For a long time I was using a free checksum tool from corz.org which does exactly what I needed, generates one checksum for an entire directory and all its contents (recursive). However, I experience some problems with it, especially when verifying a particularly large archive with hundreds of thousands of files in it... it often locks up or simply disappears.

Anyone know of any other similar software which can do what I'm looking for?

Although, I see the thread below about backup software and wonder if I should just use something like DirSyncPro to generate the differences. I wonder if it actually compares files via checksum or just size/date?

Thanks!