Download UGENE 1.11.1 package for linux:
http://ugene.unipro.ru/downloads/ugene-1.11.1-x86.tar.gz
Unpack it and launch UGENE. Set russian language for the interface and relaunch UGENE.
Result: russian letters are not shown (see screenshot).
Also, a user has the similar problem:
http://ugene.unipro.ru/forum/YaBB.pl?num=1344263122
Maybe, the resolution will be the same.