FWIW, a single-regex solution:

c:\@Work\Perl\monks>perl -wMstrict -le
"use Test::More 'no_plan';
 use Test::NoWarnings;
 ;;
 my @vectors = (
   [ 'ABC;123;;;;;HELLO;' =>
     q{ABC;'123';'';'';'';'';'HELLO';}
     ],
   [ 'DEF;345;;BANANA;12DEF;44,55;4*12;;;;;;;;3;' =>
     q{DEF;'345';'';'BANANA';'12DEF';'44,55';'4*12';'';'';'';'';'';'';
+'';'3';}
   ],
   );
 ;;
 for my $ar_vector (@vectors) {
   my ($string, $expected) = @$ar_vector;
   (my $got = $string) =~ s{ (?<= ;) ([^;]*) (?= ;) }{'$1'}xmsg;
   is $got, $expected, qq{'$string' -> \n >$expected<};
   }
"
ok 1 - 'ABC;123;;;;;HELLO;' ->
#  >ABC;'123';'';'';'';'';'HELLO';<
ok 2 - 'DEF;345;;BANANA;12DEF;44,55;4*12;;;;;;;;3;' ->
#  >DEF;'345';'';'BANANA';'12DEF';'44,55';'4*12';'';'';'';'';'';'';'';
+'3';<
ok 3 - no warnings
1..3
[download]

Notes:

• Run under Win7, Perl version 5.8.9.
• Single-quotes were used in the example code instead of doubles because Windoze command-line escaping would have made the cut-paste unreadable. Substitute double-quotes for single-quotes in the replacement of the substitution to address original problem.
• The  /r modifier for a  s/// substitution added with Perl version 5.14 makes the code slightly simpler (tested):
      my $got = $string =~ s{ (?<= ;) ([^;]*) (?= ;) }{'$1'}xmsgr;
  (See  s/// in perlop.)

Update: The regex used above has also been tested and works not only with "pure" strings (i.e., with nothing after the final semicolon), but with test strings ending in a newline after the final semicolon, as would be presumed to be the case for strings read from a file.