This posting is older than 6 months and can contain outdated information.
1) Remote Buddy is sending a "skip forward" via AppleScript to 
NicePlayer repeatedly for the length of the button press. That's all 
it can do. It doesn't have any influence on how fast NicePlayer 
executes that command nor can it know whether NicePlayer is building 
up a backlog of such commands, both of which are likely to create the 
problem for you here.
2) All "Open Remote Buddy menu" actions can be overridden by other 
Behaviours's mapping table. If you execute a long press of the menu 
button and Front Row comes up, that action is assigned to "Menu 
(held)" in the respective Behaviour's mapping table. Solution: go to 
Prefs > Mapping > "Behaviour in question" and change the mapping of 
said button from the Front Row-action to "-".
3) In the mapping area, select "Custom Actions" to create actions of 
your own from building blocks like keystrokes, delays, applescript, 
mouse wheel events, etc. It's really easy.
Regarding dialogs popping up in Awaken, VLC, etc.: these dialogs are 
not created or caused by Remote Buddy. If they get in your way and can 
only be closed with mouse interaction, you might want to contact the 
respective app authors about the respective problem(s), so they can 
either add an option or direct you to an existing option that provides 
control over this.
Alternatively, if you have AppleScript knowledge, the use of UI 
scripting may also lead you to a solution.
Best regards, 
Felix Schwarz