Sounds like the persistence of a bug from Dominions 2 (it's generally called, cleverly enough, "the scales bug") - it can be pretty annoying! Though, your scales will come back, in time...
Every time? Please, post the map and all the details you can - this bug has been in here from Dominions II, but is usually caught only after it has already happened. If you have managed to repeat this, the cause can be deduced and it can finally be solved!
Ok so further testing definitely confirms that starting a game on this province (but not other provinces around it) results in the scales droppping to base (except temperature) which fluctuates. This is across multiple attempts and in several confirming no magic sites are influencing it.
Even with dom 10 the scales vanish, pretender awake the scales vanish etc...
I include here my test file which will force any water nation to start in the province that I found causes the bug. I think I have provided all the necessary files to help debug this issue.