Maybe something like:

c:\@Work\Perl\monks>perl -wMstrict -le
"my $s = '1 x 12 x 123 x 1234 x 12345 x 123 x 1234 x';
 print qq{'$s'};
 ;;
 $s =~ s{ \b (\d{3,4}) \b }{<a $1><b>$1</b></a>}xmsg;
 print qq{'$s'};
"
'1 x 12 x 123 x 1234 x 12345 x 123 x 1234 x'
'1 x 12 x <a 123><b>123</b></a> x <a 1234><b>1234</b></a> x 12345 x <a
+ 123><b>123</b></a> x <a 1234>
<b>1234</b></a> x'
[download]

(with the HTML tags simplified). I.e., just make one substitution pass through the string instead of many.

Update: Or did you mean that you do not want the second instances of '123' or '1234' in the string to be en-tag-ified?