In iWork 2013, Apple recently changed KeyNote 6.0, Pages 5.0, & Numbers 3.0 to save files in a "package" format. A package is a directory which Finder represents as a single file. (To view the actual files in a package, right click on a file and select "Show Package Contents".)
As a result of this format change, iWork "files" will appear as a directory to other applications including Egnyte. An iWork "file" can be synchronized to the cloud by syncing all the files contained within a directory. Alternatively, you can save an iWork "file" as a zip to ensure that it is synced as a single file.
Refer to the Apple KB article below for detailed info.
We currently do not recommend editing iWork 2013 files while simultaneously running sync due to the recent changes to iWork. We are working to improve support for this new format and will post updates to this page.
Update 10/17/14: With the recent release of Apple Mac OS X Yosemite, the new iWork updated their file formats allowing them to work with Egnyte Sync applications. Users will need to update to Yosemite and update iWork to the latest version.