When your new messages appear to be archived, it's in fact a result of Gmail's handling of archived messages. Instead of a folder entitled "All Archive" or “Archive”, like most other email providers, Gmail has a section entitled "All Mail". True to the name, this contains all messages, new and archived alike.
Since our app supports many different types of email accounts, corner cases and caveats arise from time to time for different configurations. In this specific case, we use the “All Mail" folder from Gmail to show messages in our “All Archive” folder. While it may be a bit misleading or alarming to see all of your messages there, we assure you that they haven't actually been archived – it's simply a compromise we've made with our top level navigation to provide a great experience across all mail providers.