I would look in the code. Mostly, the code that does the fetch, but maybe also the code that does the output.
Please reduce your code to 20 lines or so, preferrably a self-contained program, so we can easily reproduce your problem. If that's not possible, modify your code so it uses a hard-coded SQL statement, and show the part where you fetch the data and the part where you output it, and how they interconnect.
Also, a select count(*) ... might tell you whether the database tells Perl the same number of rows it tells phpmyadmin.
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