Like month or less ago strange small window appears like every hour or 30 minutes. About describing it its like system error window like this, i mean size and it apears 2 times for 1 second or less with gap of 3 seconds in 1 hour. I can see clock icon instead of that X icon in that example pic and it says please wait... . Thats all what i can read during so short amount of time, maybe anyone had problem like this? I checked every single system process i dont know what it does and there is no useless processes but this is appearing still, main problem for me that it minimizes LFS or other games or full screen aps

Hit Print Screen next time it happens and post it here.

I had a similar problem and it was spyware.

try HiJackThis, it gives you the list of running processes that you can post on their special webpage, it will tell you if something is spyaware