We are sorry that you are having trouble with Easy Updates Manager. Hopefully we are able to get this sorted out so that you can continue to use Easy Updates Manager.
First off, what plugin are you referring to that was auto updating? If it is a premium plugin then it could be that they use a different update mechanism that Easy Updates Manager does not support.
Also, what version of Easy Updates Manager are you using? I would assume you are using 5.3.2.
Lastly, when did it stop working? Did you install Easy Updates Manager and it didn’t disable the automatic update at all? Did you have Easy Updates Manager installed and working and then when you updated to WordPress 4.4 it stopped working?
Sorry for the inconvenience.