You need to keep in mind, though, that the factors of 9999999999999999999999999999999999999999 need to be found somehow. Sure, one can "cheat" and use the factors of 1111111111111111111111111111111111111111 and a couple of extra 3s, but, then you have avoided the problem. That is fine normally, but just not an apples-to-apples comparison.
I also think repunits are, in general, easier to factor because ones that do not have a prime number of digits have obvious divisors.
Certainly, rep units of up to 50 digits are factored easily (Google a bignum factorization program online, and try for yourself)
Even disregarding that, the original code computed a square root about sqrt(n) times (that's why its running time went up by a factor of 10 for every two digits added). Even without using advanced factoring algorithms, you can factor that number using, at the very most, sqrt(n) trial divisions.
