Missing airmiles and proving I actually flew

Hi All
Looking for some advice please! I flew return LHR to JFK for three weeks in January. My original booking was economy outgoing and premium economy return. I also paid to check in a second piece of luggage for the outgoing flight.
A few days before the flight I got a courtesy call and ended up upgrading the outgoing to PE. When I upgraded I was assured that the fee I'd paid for the second piece of luggage would be refunded.
A few weeks after I returned, I noticed my airmiles and tier points hadn't been updated, plus I still had no refund. I called customer service and after a long search the [very pleasant] agent said that the reference number I had didn't exist on her system, and she couldn't even find my name on the manifest!
She advised that I email customer relations with scans of my boarding pass, which I still had. I did that on 19th Feb and got an auto email on 26th Feb confirming receipt of the email and stating I would get a response within 28 days. Just about there now, but I still haven't heard from them.
Are they generally slow, or does it really take this long to track down a passengers name on a list? I'm planning give them another call next week, if I don't hear from them but does this happen often? I was able to do OLCI and had no problems with boarding either flight, so I find it a bit odd. OLCI even shows on my flying club account history (although no points).
Has this ever happened to anyone else?
Looking for some advice please! I flew return LHR to JFK for three weeks in January. My original booking was economy outgoing and premium economy return. I also paid to check in a second piece of luggage for the outgoing flight.
A few days before the flight I got a courtesy call and ended up upgrading the outgoing to PE. When I upgraded I was assured that the fee I'd paid for the second piece of luggage would be refunded.
A few weeks after I returned, I noticed my airmiles and tier points hadn't been updated, plus I still had no refund. I called customer service and after a long search the [very pleasant] agent said that the reference number I had didn't exist on her system, and she couldn't even find my name on the manifest!
She advised that I email customer relations with scans of my boarding pass, which I still had. I did that on 19th Feb and got an auto email on 26th Feb confirming receipt of the email and stating I would get a response within 28 days. Just about there now, but I still haven't heard from them.
Are they generally slow, or does it really take this long to track down a passengers name on a list? I'm planning give them another call next week, if I don't hear from them but does this happen often? I was able to do OLCI and had no problems with boarding either flight, so I find it a bit odd. OLCI even shows on my flying club account history (although no points).
Has this ever happened to anyone else?