I tried to use the MEGASync client on multiple computers running Ubuntu to sync up a common directory of content to the cloud. I noticed that on some of them the clients it would sync only the first time and not do anything after that!
This one is a very silly bug in their client. It downloads the content the first time the sync directory is created. However, it forgets to enable that directory for syncing in the future!
To turn it back on, go to Settings -> Syncs. Tick the checkbox that is beside your sync directory and click Apply. That is it!
Tried with: MEGASync 2.6.1 and Ubuntu 15.10