When to pay excise tax on refunds

If there was an ADP failure and the TPA refunded the refund amount prior to 2 ½ months after year end but didn't refund the earnings until 3 months after year end, do you have to pay excise tax on the earning portion that was not distributed prior to 2 ½ months or is excise tax only due on the refund amount? 

Excise taxes are on excess contributions, not earnings. But if you only did a partial correction by 3/15 - not ALL of the excess contributions AND earnings then you have not corrected by 3/15. I think IRS would deem the pre-3/15 payment as a combination of contributions and earnings such that the post-3/15 payment would have a contribution component. 

For example, if you paid $9,000 of excess contributions by 3/15 and then $1,000 earnings in April, I think you really corrected 90% or $8,100 in contributions by 3/15 and have $900 after 3/15 subject to excise tax. Maybe I'm wrong, but IRS generally does not favor partial corrections.