This is odd, because the problem seems to be specific to you. There are others even using 64-bit windows builds who are not experiencing the same issue. It's very hard to track down what is causing this when no one has been able to reproduce the issue so far.
Can you do something for me: uninstall LMMS completely, get rid of the entire LMMS installation, the settings file, everything. Then try to re-install the new LMMS 0.9 build, 32-bit version just to be sure.
Then try something: play the VST instrument first with the regular computer keyboard, then try playing with the mouse the virtual keyboard in the instrument window itself, then try your MIDI keyboard. Is the issue the same way accross all these input methods?
Can you do something for me: uninstall LMMS completely, get rid of the entire LMMS installation, the settings file, everything. Then try to re-install the new LMMS 0.9 build, 32-bit version just to be sure.
Then try something: play the VST instrument first with the regular computer keyboard, then try playing with the mouse the virtual keyboard in the instrument window itself, then try your MIDI keyboard. Is the issue the same way accross all these input methods?