MSE doesn't catch everything. I've been running it for a couple of years on Win7, and a few months ago discovered I had several little pests that MSE never detected. It took MalWareBytes to find and remove them - 3 full scans of mwb. By the 4th everything was clean. 

I discovered all that due to problems with my mouse double clicking. Apparently viruses can cause a mouse to seem like it's dying or wearing out when in fact it's just a virus. Everything I was googling kept saying to replace the mouse because the spring was worn out. Once MWB did all it needed to do the mouse worked just fine.

 

~Shane