Blocker If there are several UGENE versions with the same version, then there could be troubles with plugins loading.
UGENE writes paths of its plugins to the settings file. During the next launch it reads these paths and unites them with paths to plugins that UGENE found in the "plugins" folder. Usually these two lists are absolutely the same. But if you have another UGENE instance somewhere else, then these lists will differ. In this case some plugins won't be loaded.
Plugins IDs should be checked. If there are duplicates, plugins from the "plugins" folder should have higher priority to be loaded.