Box 12 code W should include contributions made by your employer as well as contributions made by you via a salary reduction agreement (aka cafeteria plan) through your employer. For the purposes of Form 8889, you would include box 12W amounts on line 9, not line 2. However, all contributions (employer, employee, pretax or after tax) are subject to the overall contribution limit. My guess is your previous employer should have reported their $1000 contribution in box 12W.
Also, are you saying that there was a total contribution of $5750+1300 through employer #2, or is the $1300 included as part of the $5750? If your total contributions for the year were $1000+1300+5750 then you may owe some sort of penalty for excess contributions.