Mouse Opens A Window, However Cannot Click Inside The Window

I am running into an issue where I can open a window/program with my mouse however once the window is open I cannot click inside of it. The window becomes inactive. I also have noticed I cannot right click on my desktop to bring up the properties. I can right click on the window in the task bar to close it but not in the window. Since this is happening I am limited to command prompt. I ran sfc /scannow with no errors. I tried with 3 different mice. I booted the computer into safe mode with command prompt and brought up the device manager to show devices not in use, and when the device manager window opened I could click inside it! since I could use the window I uninstalled all mouse drivers, and reinstalled my microsoft wireless usb mouse driver.. while in this safe mode I changed my mouse properties to system default as I read somewhere that can reset things. Next I booted the computer in safe mode (without command prompt) and still the same thing. I was trying to do a restore point as well however my Kaspersky antivirus 2012 is preventing that as i cannot find a way to kill the program through command prompt.