Get a better keyboard that doesn't repeat punctuation characters.

Don't use C for loops. Avoid rewriting the same code. Use English prose white space conventions where applicable. A little restructuring gives:

use strict;
use warnings;

my @run;

for my $element (@run) {
    my ($run_cmd, $chdir_cmd) = split ';', $element, 2;
    ch_dir ($chdir_cmd, $patch, '0');

    system ($run_cmd);
    if ($run_cmd =~ /check.pl/) {
        next if $? == 2;
    } elsif ($? == 0) {
        next;
    }

    print "Command Failed: While Executing $run_cmd$!\n";
    $err = 1;
}
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which is of course incomplete and untested.