Shopify filters out duplicate shipping rates based on shipping rate title.
So if you have two rates:
Standard Shipping
Standard Shipping
Only one will show.
This can be a problem when testing rates where you have re-configured your existing rates into the app with the same title.
They don't even need to 100% the same, Shopify will sometimes just look at the first several characters/letters of a shipping rate title and filter one of them out.
So if you have two rates:
Express Two Day Shipping with Tracking
Express Two Day Shipping without Tracking
Shopify may filter one of the rates out.
To check if it's the case, give the rate that you aren't seeing a completely unique shipping title, then bust the shipping cache, and see if it shows up. If it does, then the issue is a duplicate or 'too similar' rate title.