Okay, ideone.com is running on 32bit, and that is what you're running into. On my 64bit system with this input:

9 7
900000000000000009 900000000000000007
99223372036854775810 99223372036854775808

2 2 2 2
2 2 2 2
0 0 0 2

Seems that there is a problem with magic: if use bigint and take some string, Perl doesn't convert correctly string to bigint?

Yes, unless one of the variables has already been coerced to be a bigint, so even this is enough:

use bigint;
while(<>) {
    my ($a, $b)= split/ /;
    $a += 0;
    print $a - $b, "\n";
}
[download]

However you can just coerce everything when you first read them in as strings:

use bigint;
while(<>) {
    my ($a, $b)= map { 0+$_ } split/ /;
    print $a - $b, "\n";
}
[download]