Oh by the way, the travel agent still insists he will refund the money when my wife is here. He will only pay after seeing the receipts. All verbally...
On my insistence that he should give this to me in writing, he straight away declines and keeps on saying we should trust him.
And that is funny.....very funny...
I am sure there is a clause which he will use to just walk off scot free without paying a cent.
If anybody in CD knows about airline clauses please do let me know.
I really fear small print clauses in N. America..

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"After climbing a great hill, one only finds that there are many more hills to climb." (Nelson Mandela)

Just an update on this:
Emirates Africa have been sending a lot of emails to Head Office in Dubai explaining the situation. Asking that my wife should not pay and they should directly take the money from the travel agency.
The guy making this decision is still slow to respond and that is what we are waiting for now.

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"After climbing a great hill, one only finds that there are many more hills to climb." (Nelson Mandela)

From what you have explained it seems everything else is OK but only wrong stationery was used for printing tickets.

Airlines have a vicarious liability/responsibility for actions of their agents also. In this case they should just let you fly without any payments whatsoever and the agent should be pulled up for inconvenience caused.

Also meanwhile you can tell the travel agent to call Emirates office in Dubai and get the things set right.

Best of luck.