In Lotus Sametime 7.5 or higher, select preferences, then notifications. Click on the “event” you want to modify from the list on the right side (e.g. one-to-one chat) and you should see options for whether you want it to come to the front, flash on the screen, play a sound, etc. Repeat for the other event types (incoming calls, multi-person chats, etc.)
I’m sorry, but I no longer remember how to do this on older clients.
I am assuming that you are using Lotus Notes Sametime version 8.0
Hopefully this should have resolved your issue.
For Sametime version 8.5.2
Go to Preferences -> Notifications -> Select one-to-one chat
and disable “Bring window to front on new chat”, “Bring window to front on chat response” checkboxes
same for Multi-party chat
Go to Preferences ->Notifications -> Select Multi-party chat and disable the checkboxes as mensioned above.