For example, I don't understand how to proceed in some situations. Let's say A:B and B:C have been processed. Now A:B:C is read from the input - what should happen with it?

My apologies for some of the ambiguity, I'll do what I can to clear it up. From the data, only one new group is added at a time, and it will never include parts of an group that has already been established eg. if A:B has been looped through B:C or A:C cannot exist, but C:D can. Only one new group or single element are added at a time. Here's an example list of what I mean: 51:50, 51:50:47, 51:50:47:42, 37:30, 51:50:47:42:37:30 and so on. Here's my current loop which only works for groups of two such as A:B.

 foreach (0..$#names) {
    my $dist = (($distances[$_]*$xaxisstep)+42);
    my @tmp = split /:/, $names[$_];
    my @tmp1;
    if (($#tmp+1)==2) {
        foreach (@tmp){ 
            $_++;
            print PS " 42.00 $labelmarks{$_} mt $dist $labelmarks{$_} 
+ls\n";
        }
        print PS " $dist $labelmarks{${tmp[0]}} mt $dist $labelmarks{$
+{tmp[1]}} ls\n";
        $xlabelmarks{$tmp[0].":".$tmp[1]}= $dist;
        $labelmarks{$tmp[0].":".$tmp[1]} = (($labelmarks{$tmp[0]}+$lab
+elmarks{$tmp[1]})/2);
        delete ($labelmarks{$tmp[0]});
        delete ($labelmarks{$tmp[1]});    
    }
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Sorry, but your description is still quite unclear and your code does not run because it contains a lot of variables that we don't know about (I'm going to guess they aren't relevant to the question either). If you could please reduce your problem down to: short sample input, runnable code, the expected output for that input, and the actual output you're getting, including any error messages, each within <code> tags. As choroba already said, please read SSCCE, and also How do I post a question effectively?.

Just for fun, I'm going to take a guess at what you might mean. Note this is a brute force approach that I just whipped up, there's probably a much more intelligent algorithm than this.

use warnings;
use strict;

my @input = qw/ 51:50 51:50:47 51:50:47:42 37:30 51:50:47:42:37:30 /;

my %seen;
for my $in (@input) {
    my @items = split /:/, $in;
    my @subsets;
    for my $start (0..$#items-1) {
        for my $end ($start+1..$#items) {
            push @subsets, join ":", @items[$start..$end];
        }
    }
    @subsets = sort { length $b <=> length $a } @subsets;
    my @seen;
    for my $subset (@subsets) {
        push @seen, $subset if $seen{$subset}++;
    }
    if (@seen) {
        my $new = $in;
        my ($re) = map {qr/\b(?:$_)\b/} join '|',
            map { quotemeta } @seen;
        1 while $new =~ s/$re/:/g;
        $new =~ s/:+/:/g;
        $new =~ s/\A:|:\z//g;
        $new = length $new ? "'$new' is new" : "nothing is new";
        print "In '$in', I've seen ", join('/', map {"'$_'"} @seen),
            " before, $new.\n";
    }
    else {
        print "I have not seen '$in' before, it is new.\n";
    }
}

__END__

I have not seen '51:50' before, it is new.
In '51:50:47', I've seen '51:50' before, '47' is new.
In '51:50:47:42', I've seen '51:50:47'/'51:50'/'50:47' before, '42' is
+ new.
I have not seen '37:30' before, it is new.
In '51:50:47:42:37:30', I've seen '51:50:47:42'/'51:50:47'/'50:47:42'/
+'51:50'/'50:47'/'47:42'/'37:30' before, nothing is new.
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