Okay.
Firstly, your example which does not work either, is different from the first example. The first example was

$number=1234567; # with commas, should be "1,234,567"
$number =~ s/(\d)(?=(\d{3})+(\D|$))/$1\,/g;
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Which will result in the string 1,2,3,4,5,6,7; Not quite what we were looking for.

Your second example both extends the string and adds a decimal portion, and does not work either.

$number='1234567890.01';
$number =~ s/(\d)(?=(\d{3})+(\D|$))/$1\,/g;
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Resulting in 1,234,567,890.0,1; You will notice the comma in the decimal portion of the resulting string. I find it strange the the output you presented in your message is correct. Did you paste it from a run, or transcribe it and introduce the alteration in the result by accident? As pointed out by Anon, if you introduce a few more decimal places you will end up with more commas in the decimal portion.

$number='1234567890.0123456789'; # with commas, should be "1,234,567,8
+90.01
$number =~ s/(\d)(?=(\d{3})+(\D|$))/$1\,/g;
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Resulting in 1,234,567,890.0,1,2,3,4,5,6,7,8,9.

The problem comes in because we are testing against \D|$ to determine when to place to commas. This allows commas to be placed in the decimal portion. I don't have a great solution but you can do something like the following:

$number='1234567890'; # with commas, should be "1,234,567,890.01
$number .= '.' if ($number !~ /\./); # Make sure we end with a decimal
+ if we don't have a decimal
$number =~ s/(\d)(?=(\d{3},?)+(\.))/$1\,/g;
chop $number if ($number =~ /\.$/); # Get rid of that useless trailing
+ decimal
print "N  $number \n";

$number='1234567890.01234567687'; # with commas, should be "1,234,567,
+890.01
$number .= '.' if ($number !~ /\./);# Make sure we end with a decimal 
+if we don't have a decimal
$number =~ s/(\d)(?=(\d{3},?)+(\.))/$1\,/g;
chop $number if ($number =~ /\.$/); # Get rid of that useless trailing
+ decimal
print "N  $number \n";
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The are better solutions presented, I just wanted to respond to why this example did not work.