The provision that allows you to make HSA contributions as late as October 15 of the following year, only applies to direct contributions by you. As far as I know, the employer does not have any such leeway with respect to the salary reduction agreement that they must enter in with you under section 125.
[Edited to correct] The employer may make contributions as late as April 15 of the next year, designated for the previous year.
And in any case, if you don’t meet the qualifications to earn the employer contribution, they don’t have to make one for you. IRS regulations require that employers treat all employees equally in order for the benefit plan to qualify for special tax treatment. The definition of what constitutes equal treatment depends on what is written in the plan documents and any employment contract you might have. For example, if the plan rules say that you will only be credited the $1000 benefit if you are actively working as of November 1, and you were on medical leave on November 1, then you don’t qualify under the plan rules. If you can show, the employer is not following the plan rules, you could make a case to the state labor board or sue them, I suppose.
