mine is like that too. i just use the webui.
Have you tried changing the resolution on your box or pc??
Im guessing the resolutions are set differantly and thats causing the issues.
first you need to kill your vncserver (vncserver -kill :x) "x for the vncserverport"
then install twm in putty (yum -y install twm)
after this start a new vncserver (vncserver :1)
then start utorrent
and you can scale the windows in vnc
dont kill anything, thats absolute nonsense
just make sure the resolution on the box and ur pc is the same