In addition, you are unnecessarily putting your variables inside double quotes. So your line

$bedgenenames{"$array[3]"}="$array[6]";
[download]

can just be

$bedgenenames{$array[3]}=$array[6];
[download]

And I echo what someone else has said already -- get friendly with the debugger. It's most illuminating to step through your program and see what's going on.

Finally, Perl hashes may not be perfect, but they are pretty reliable. If your code isn't behaving correctly, it's most likely that the fault is with your code, and not Perl itself.