Even in the box-regularized case you get an infinite ground-state energy when doing the calculation in a naive way. The reason for this failure is that the field operators in quantum field theory are operator valued distributions, which you cannot multiply in a mathematically rigorous way. That's why already at this stage you have to renormalize by subtracting the infinite zero-point energy. As long as you neglect gravity, there's no way to observe the absolute value of total energy. Only energy differences between different states of the system are observable quantities, and thus there's no problem in relativistic QFT with the infinite zero-point energy arising from the sloppy calculation of the operator of the total field energy (the Hamiltonian of the free fields in this case).
In cosmology, where General Relativity becomes important, there is a really big problem with this, because even when renormalizing the zero-point energy you need to adjust the corresponding parameters of the Standard model to an extreme accuracy. The reason is that the Higgs boson is a spin-0 field and it's mass is quadratically divergent. This is known as the fine-tuning problem. The question thus is not, why there is "dark energy" but why is it 10^{120} times smaller than expected. It's one of the least understood problems in contemporary physics. A famous review on this issue is
Weinberg, Steven: The cosmological constant problem, Rev. Mod. Phys. 61, 1, 1989
http://link.aps.org/abstract/RMP/V61/P1