How to prevent Numbers from changing currency automatically
I have a similar problem which may be related. In my case Numbers 4.3 allows me to specify the ratio of two currency cells as a number or a percentage but then immediately and automatically reverts the cell back to the currency format of one of the origin cells. I agree that Apple Developers are probably trying to 'help' (but don't realise that they don't yet have the competence to do so infallibly). 

I have reported the problem via Apple's Feedback on:
 https://www.apple.com/feedback/numbers.html 
and suggest you do likewise. The more of us that report it the more likely they'll sort it. 
Meantime I have had to remove the currency format from my origin cells and added it to the description in the row/column headers. (Not ideal, I know.)