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@z.nina: what filesystem is used on the second drive? I ask because on Windows, whenever the database is changed the database manager (sqlite3) creates a log file, writes recovery information to it, changes the db, then deleted the log file. It you are using an odd file system then that create/write/delete cycle could be the culprit. If you are using NTFS, it probably isn't the issue.
Another thing to check is whether write-behind caching is turned off on the second drive. Go to the device manager, right-click on the disc in question, choose Properties, and check in the "Policies" section. Turning off write-behind caching would be catastrophic for calibre performance.
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