Well since the docs arent gonna be up until tuesday ill just tell you people what the colours mean in the tray icon.
Green: Scanning files
Red: The menu is open or malware found. (probably in the background if you cant see it.)
Black: Nothing happening right now.
Hope this helps a bit.
Ah thnx m8 
But do you know what Blue means ???
Greetz, Red.
hmmmm blue, havent got blue yet. What were you doing at the time when it went blue?
Green or blue, you’re talking about the same thing:
A blue or green colored "flick" of the traybar icon will be noted when BOClean does this recalibration every ten seconds.
Let’s call it blueish green or greenish blue instead… ;D
Lol Thank you TonyKlein
Greetz, Red.
You’re very welcome. 
(P.S. I think it’s blue as well…)
Turkoise?
Lol Nope it’s not you or me After you check for an update the icon is green. And when you close the menu after checking for an update the icon is blue for a few seconds. At least I know now what it is doing
Greetz, Red.
Wow, I do believe you’re right. Wad’ya know: a new feature after all! LOL!
Maybe you thought I am coulorblind or so :o I am Dutch too you know Stupid maybe, but not coulorblind 
Greetz, Red.
For all of you playing the home game along with this pixmission, since I’m the one who wrote it, I have the secret decoder ring right here … no wait, it’s in my other pants.
Green=examining startups (goes fairly quickly)
Blue = examining processes, threads and dependencies
Black = quiescent (nothing going on)
Red = detection has occurred OR you’ve opened the menu and BOClean is on hold until you close it.
On starting the system, it will be blue for quite some time as BOClean actually starts green but that’s usually over by the time the traybar icon appears on bootup. Blue sits there for quite a while as BOClean examines every single process, thread and dependency at startup. Once all is done, it settle into black unless something is started or it does its every ten second “recalibration” … when this happens, you’ll see a fast green or blue flick - starts green, goes blue but it happens so quickly if nothing’s happened in the past ten seconds that you might see one color or the other or a combination of both (particularly on LCD screens) … if anything starts or changes, it doesn’t wait for that ten seconds so you’ll see that flick should ANYTHING move or start.
Final answer?
Final answer, Regis. (:NRD)