In your first version you use %_ to store data, which is a strange choice of variable. In the second version you use @_ to store your data which is very strange and - as you found out - has funny side effects. I have not really looked at your code but using $mat[$tc] instead of $_[$tc] everywhere should solve your problem.
UPDATE: In your subroutine
sub add{
my ($i, $j, $add) = @_;
$_[$tc]{value}[$i][$j] += $add;
}
you are even referring to two different @_ arrays explicitly. The one that passes the parameters into the subroutine and the global one that you use to store your data.
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