Chantelle, our FA told us that it was the Malta system that had gone down....nothing to do with BA. That was also the message given by the FO,Pilot as CSM. However, the other flights checking in didn't seem to have the same problem.
I'm not sure how the crew would know better than the ground staff, but going by the near daily problems with the new system, it would be safe money that it was the BA system that was down.