I have a system running server 2003 and backup exec 9.0.
I am seeing occasions that when back to back jobs running with an autoloader lto will overwrite the tape from the first multitape job in the second job. This occurs even when other none used scratch tapes are available in the cartridge.
Also, v9.1 will accept all your v9 serials, so may be worth upgrading, tho I've never heard specififcally of this problem, so don;t know if it would have any effect.