Form 8606 line 2 should not show any of the money that came from the 401(k) unless you had after-tax money in your 401(k) (most do not). It seems that somehow you entered an incorrect amount of traditional IRA basis after clicking the Continue button on the Your 1099-R Entries page. Also make sure that you did not enter under Deductions & Credits any of the rollover amount as a new IRA contribution. Go back and review your entries.
