This is the "DSOD". Look it up for discussion in other threads. It's not related much to any specific software. The problem seems to be twofold, both a problem with the default sync schedule with Activesync and an apparent bug with the storage card drivers. It's most likely going to take a rom update to solve the problem completely even though most have almost completely eliminated the problem through the various posted hacks.

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AT&T iPhone 8GB, Belkin leather case