The internet here is bad.
When it was first installed it was very fast; seemingly close to the maximum of 12 Mbps in Misa's plan. Over time it's become slower, and worse, the connection sometimes drops. After enjoying the steady-state and high speeds of fiber optic it has been a bitter pill indeed.
Things appear likely to improve before long. I hesitate to be jubilant as we were close before, but Misa has been doggedly assaulting the involved service providers' customer service blockades. It looks like for about ¥300/month I can keep my old email address even after the switch to the building's contractual provider.
So some time in the next month or so, the unstable SKYPE-ing should cease.
For those outside Japan:
Connection speeds are comparatively good here for the cost, but installation/modification of service tends to take a few weeks (at least).