Nothing is left after a full flash. Unless you have data sitting off somewhere after a flash that can be auto-accessed, doing a restore, etc, nothing should be left. If it is, then something is very wrong.

Contacts showing up again I might believe, if one of the PRs introduced the ability to read contact info off the SIM. I haven't flashed since PR1.1, so if something after that added a SIM import, that could affect contacts. But then N900 isn't known for having SIM tools, so I doubt that one too.

Very likely the data is coming from an external source. Be that a memory card, or a network thing, or bluetooth/usb sync. Do you have a memory card in the uSD slot? If so, have you done this with the card removed? Are you running sync on the PC you're flashing with? Do you have another machine setup to sync over bluetooth? Is either set to auto-sync on connection? Is it syncing after the flash process, but before you're noticing it? That would update your contacts, and maybe some shortcuts, like rss feeds & browser bookmarks.