Interairline baggage checkin with two tickets
 

I recently run into this problem with Jetblue. My wife had two separate tickets. One on Jetblue from MCO-JFK and then another one on their partner airline Emirates from JFK-DXB-CCU. When i called earlier in the AM i was told that baggage could be through checked from MCO to CCU. When i arrived in MCO the jetblue person told me that was not possible.

I requested to speak to the supervisor who proceeded to tell me that according to IATA rules that was not allowed. I cut him short since i have done that many times before in my travels (I am million miler in Delta, 1K in United and Executive Platinum in American). He then sarcastically told me that he could cancel my tickets!

I tried to call up Jetblue to get clarification but they had a 30 minute wait. So i had to relent and she had to book the heavy bags to JFK.

Needless to say i was livid at being treated like this (should not have been surprised from an airline that keeps their passenger locked up in a plane for 7 hrs in a snowstorm!!). I have filed a complain with the airline though I doubt that will lead to any reasonable resolution.

I guess I will just have to never fly these guys again! Any guidance on inter airline baggagle handling with multiple tickets would be appreciated. I have not run into this issue before!

Welcome to Flyertalk.

The two tickets may have been the problem. They define interline as

Interline flights are flights that are on the same ticket as your Emirates flights, but operated by another airline and do not have an 'EK' flight number. These airlines may have a different baggage allowance to Emirates. Refer to the Interline Partner Baggage Allowance page for information on the allowance or charges for carry-on baggage and the first and second checked bag.

Interairline baggage checkin with two tickets
 

Let me add a twist. Were you polite? Flashing status on face doesn't really board well with most airline employees. I ask this as you mention that he 'sarcastically mentioned that he could cancel your tickets'.
I have been in similar situations numerous times and never had an issue. Just be ultra polite as you are on the receiving end. I doubt you will get any positive resolution in your favor.

I had the same problem 2days ago with united and US Airways and i was told as per TSA rules and regulations they are not allowed to check Bags all the way thru if the segments are not on the same ticket.There were a change last Septemper so i was told .

The only time I had issues was when flying AK and WN. Both carriers specifically do not interline.

I have done CX-UA, UA-AA, CX-LX, SQ-AA in 2012 without an eyebrow raised. I always present both tickets at the same time.