Gmail labels creates duplicate emails when having more than one label. I quite extensively have used Gmail’s labels just as such, labels, and not think of them as folders. It’s very handy to e.g. label an email both as eBay and PayPal for an email that relates to a PayPal payment for something on eBay. And if you “Star” that email, it gets worse as eM client creates 3 copies of the same email in 3 different folders. This can especially be seen on the Agenda pane of the right if you have a message both starred and labelled: it appears twice. I have many many emails in 3s and 4s in that list. Why can’t eM client simply see it as one email with several labels, instead of equating labels with folders, which is not the way Gmail works?
unfortunately this is a standard behavior for eM Client at the moment. You can turn of the “starred” and “important” labels in Gmail so you don’t get those duplicated, but if you use multiple labels on one email it will behave like this.
It’s not an issue at the moment, but there might be a better solution to this in the future. If you’d like to see this feature in eM client as soon as possible, create an “Idea” topic and let other users vote for the suggestion.
Thank you for understanding,