You've almost diagnosed the problem correctly, but not quite. When Perl turns the string "1,000" into a number, it does not think it is reading a list. What happens is that, since ',' is not a valid character in a number in Perl, the string-to-number conversion just stops when it gets to the comma. This would be the same as '1j000' or '1~000'.
You don't show where your numbers are coming from, but you can avoid this problem by removing the commas from your 'numbers' before you use them as numbers:
$num =~ tr/,//d;
Of course, it would be simpler to not put the commas there in the first place.
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