Well, that's good news then. I can tell you how it can be done. Right now it's a workaround, but in an upcoming release we will be fixing it to work in the dist kit dialog.
OK, so what you want to change is the sub folder of the Start menu icons to be "Suite Name"\"Program Name". This is set under the Advanced... settings and is called Start Menu Sub-folder.
1) Go to the Advanced settings and uncheck Use Default for Start Menu Sub Folder.
2) Now, unfortunately, this dialog will not let you type in characters like "\" (this is what we are fixing), so you have to work around it. Type in REPLACEME in the sub-folder name.
3) Now Close the Dist Kit dialog and close the project.
4) Open the PRJ file in an editor like Notepad.
Search for your "REPLACEME" string and replace it with your subfolder name "Suite Name"\"Program Name".
5) Save the PRJ file and go back to CVI and build the distribution kit.
That should installer should put the program icons under Start->Programs->"Suite Name"->"Program Name".
Let me know if you have problems,
Chris Matthews
National Instruments