I also had this happen to me, on Dwilight. My region would increase to around 5,500 population (out of a maximum 6,300) and then rapidly diminish back down to about 5,000, before starting the cycle again. Recently the population crashed further than usual, and is now 4,500~. There is no report of this population loss in the region reports, so I can only guess as to the cause.
As far as possible explanations go, here's what I will rule out:
Recruitment: there are only 2 recruitment centres and I don't see how they could drain 500+ population in such short periods of time, with such intermittency.
Police action/looting/monsters/undead/starvation: none of that happened.
The only thing that I can think of that could cause the population loss is emigration. While I don't get any notices of emigration, all of the regions surrounding mine are depopulated, so it would be plausible that my region's population is spreading to those lands without notifying me.
