Sounds like this program needs a C or D grade if it's flagging 12% of 16GB as a problem. That's just a load of crap no matter how you look at it.
I also don't buy the fragmentation postulation put forth. If you have 16GB of RAM, then almost guaranteed you have a HDD that's quite capable of overcoming a little fragmentation.
I think the answer's really simple, and you're just putting way too much faith into this one program. Which is to say putting ANY amount of faith in it. Given it's flagging 12% of 16GB as a problem, I wouldn't at all be surprised if the program is rigged to show you that your system performance degrades over time... And then guess what? It just so happens they have a program which will get your system ship shape in no time, that they'd be willing to sell to you for $40 or whatever. Probably the only thing that program actually does, is reset some counter on the other program so that you get a better score. This has all the hallmarks of your classic scam. I would say you should cut your losses and run at this point.
Using advanced systemcare I noticed today my grade is always C or D. Checking their monitor the only 2 things were out of place I guess: the memory usage was 12% of my 16GB total, and disk usage jumps to 100% from time to time.

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