As you have noted, the cog in the menubar is a new feature of Yosemite that alerts you when certain network tools are used. It does not seem to be something one can currently turn off. Since it is not part of IP Scanner it is also not something we can influence.
Here's what we think is happening: any time a network tool like arp or ping is used the cog now pops up. Since IP Scanner uses a lot of network processes, that cog shows up a lot. However, the cog should disappear when the process it is monitoring ends, and certainly when the app quits. However, it appears that the monitoring process that initiates the cog is perhaps itself buggy because it should not be possible for threads initiated from an app to keep running outside of the scope of that app - those should all get killed by the kernel when the app exits.
We are continuing to monitor the situation, and have released version 3.28 of IP Scanner, which imposes some limitations on how long threads can live to hopefully limit the time the cog displays when ping or arp or another network function is stuck: http://10base-t.com/downloads/.....r_3.28.zip