Hello,

the main point is that the best way to install UGENE is by using installers - you may download them from there http://ugene.net/download.html Version you installed with PPA is a bit outdated, version from installers has this bug fixed already.

Also, you may fix this problem in your version. Click "Settings" -> "Preferences..." (the first line). In the appeared dialog change "Appearence" to Fusion (see the attached picture) and click OK.