This sounds like my issue. I'm not entirely through diagnosing it, but the symptoms sound the same.
I have 2 EXT3 drives in an enclosure. They work most of the time, however (at random) during my nightly backups when the drives are hit hard they will dismount and re-mount.
I usually have 2 1TB ext3 mounts sda1 and sdb1. The failure manifests in one of a few ways:
1) sda1 becomes sdc1 and is still accessable.
2) sda1 simply goes away and won't re-mount ever again. I have to wipe the drive
3) all drives disappear and won't re-appear until I reboot tomato.
I'll try to get some logs. I usually panic and reboot when this happens and lose any information that might be there. This is biting me hard because I rely on this for backups and it's turning into a very unreliable system.
I know this is Tomato combined with the ASUS RT-N16 since it has happened with 2 different HDD enclosures from 2 different vendors.
There is hope: I have a USB protocol analyzer. As a last resort I can let that run overnight on the backup and probably be able to point the finger one way or the other.