Amazon has turn on Automated Handle Time in your General Shipping.

Go to Shipping Settings

Then click on the General Shipping tab

Scroll and find the box showing Handle Time

Click the edit button and turn off Automated Handle Time

Set your Handle Time (it may not revert completely back to 3 days but you should get 1 or 2 days as an option)

Now to make it so that Amazon leaves your Handle Time as 3 days, you need to set the Handle Time at item level. This can be done using the Manage Inventory Edit page for each item you want at 3 days or you can use the category specific template uploads (if you know how to work with them) and do all items at once.

Item level Handle Time overrides the general Handle Time set in the General Shipping Settings and therefore is the better way to set Handle Time (especially for custom items).