I wrote a column on that :-) (Well it was months that I wanted to say this in a node!).

This has nothing to do with MySQL. It's a DBI issue. If you fetch a record with fetchrow_hashref and you have more columns with the same name, you will get only one of them.

See DBI recipes and look, towards the end, for a section titled "A trap to avoid with fetchrow_hashref".

The solution to your problem is either using an alias in your SQL (select a.id as AID, b.id as BID) or using a different method (fetchrow_array, fetchrow_hashref).

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