If you first select another currency besides your reference currency then the currency conversion does not work. It just adds the reference currency price. To make the quote work you have to add all line items with the reference currency selected. Once you have added all the line items then you select the currency you want to quote.
This is not how Zoho worked previously. The real problem comes in when you want to update a quote. You have to re-select the reference currency, do the change and then change back the to currency you want to quote in. a ridiculous process!
I tried to get this resolved with support but we ended up talking in circles. No clue! Very irritated with the latest change.