The trick is to use variables to memorize where you are in your processing. Either use a variable that records your "status" as a number (that is called a [no such wiki, state machine]) or use one or more variables that record different conditions (commonly called "flags"). Below is your script adapted to use a flag called $foundchrom:

my $foundchrom=0;
while(my$line=<DATA>){
    if ($line=~m/^variableStep/) {
         if ($line=~m/$chrom/){
             $foundchrom=1;
         }
         else {
             $foundchrom=0;
         }
         #above if-then-else could be written shorter as
         #$foundchrom= ($line=~m/$chrom/);
         next;
    }
    my ($s,$prob)=split(/\s+/,$line);
    if ($s<$start or $s>$stop or not $foundchrom) {
        next;
    }
        else{push @values,$prob;}
    }
}
[download]