All of traditional bank accounts statements has it base currency and we have no issues in set those up in QBO.  However, various merchants accounts statements such as Paypal have 2,3 or more currencies and that's why we can't set them up properly in QBO.  

I understand it's not the problem from existing QBO but it's a matter how you will need to cope with in the future.  Right now, I may need to deal with those stuff manually until hearing a solution from QBO.  Hope to hear from you soon.

Regards

Nam Tran, CPA