The 3+ minute pause in between an obvious move

I am not an elite chess player by any means, but I do notice many of my losses include a long pause by my opponent when we are in an equal position. Go figure as soon as they "come back" they make amazing moves to destroy my position and/or gain material. I like the 10 minute game but this is going on way to often.

Supposedly, they have computer check programs to definitely prove whether a program is making the moves or not.  From what I have read even super grandmasters will only agree with a certain percentage of computer moves. 

if they gain material it is not an equal game

Computer vs. human is never an even game. They will almost always find a way to gain material over most players.

It could be , just maybe, that during that time they are making a plan .