It sounds as if the programs are being started more than once. To find out if this is so, go to 'Start/Run' type 'msconfig' in the box and click 'OK' click on the 'Startup' tab and look down the list of programs. If a program is running more than once it will show up here. Be aware that unchecking one entry may stop the program running at all.
Using TM to stop the extra items is not likely to cause a problem, but if you have multiple starts of the same software you could look here for a cure link text. Most here are for XP but without knowing you OS it is not possible to be more specific.