UPDATE: Fixed in the latest version of gogoDocs (1.1.4). Head over to the app store to get your copy.

We are currently working on an issue where a folder that was uploaded through the Google Docs web site using the new “upload folder” functionality does not appear in gogoDocs. For now, we recommend that you upload files via the two other means if you wish to view them in gogoDocs.

UPDATE:

The reason that they’re not showing at the moment is that the documents themselves, but not the containing folders are marked as hidden on upload (or “Don’t show in home”). We do some fancy filtering of the feed to remove hidden files and empty folders as Google Docs used to treat hidden files somewhat differently than they do now. Since hidden files are removed in gogoDocs so are those, now empty, folders. We’re working on an update that makes your files and folders list more accurately follow the way Google now displays them.

Workaround:

Currently the easiest way to view any files uploaded in this manner is to log into Google docs through your browser and mark each document you want to see in gogoDocs with “Show in home.” This will unset the hidden flag on the documents. You can select multiple documents to make this go faster. Here is what it looks like on Google Docs when you do this.