In Windows 7 Ultimate 64-bit SP1 launched applications use the Windows Classic theme for some of their UI elements. This applies to Launchy v2.5 and v2.6beta2
I'm not sure if it's something unique to my system, but I can confirm this behavior with many applications: for example, Notepad++ launched from Launchy will use the Windows Classic theme for all of its UI elements except for the window frame; Notepad++ launched directly from double-clicking its executable will use the Aero theme (or 3rd party theme) for its entire UI.
I've attached a screenshot to illustrate what's happening. The image on the left is of the Windows sound control panel launched from Launchy, and the image on the right is of the same control panel launched by Start Menu > Control Panel > Sound. The red outlined boxes indicate some of the UI elements in the launched application that are affected.
Comparison of app launched with Launchy vs. launched directly