I found, at least for laptops, going from quad core 4GB RAM to i7/8GB RAM let me load tons more plugins in Pro Tools. You can always change to SSD or dual drives if there's a slot. I upgraded my custom built PC though and went for RAM and hard drives and was pleasantly surprised. The PC's AMD also, and on PC I don't see a big difference. Both systems are about the same in speed now, just the i7 loads more completely different programs faster, and a few extra plugins probably. My last step is to get a better CPU for my PC. The cool thing about a half way decent motherboard is running three or four hard drives if you want, I got three now. It DOES get taxed on the CPU sometimes though with that "tons of plugins" thing mostly because my son mixes IRs in with his recordings. Too many IRs on my i7 machine will start to audio glitch too, BUT I'm still only at 8GB RAM on the laptop and 4GB RAM on the PC.

What I'm trying to say, is more than likely Singtall is correct about that. At the point you bottleneck your CPU, you're already bottlenecked from low RAM and using just one hard drive or a slower hard drive. I'm sure an i7 PC is faster than my laptop but my laptop is an ASUS G73-XA1 built to be fast for gaming, dual 7200RPM drives (SSD in the future for sure). 3 seconds? WOW. I think...it's more about the streaming speed because at the point glitches happen, there's also TONS of tracks on those projects. You're going to bottleneck if you have a bunch of tracks and the hard drives are working over time with less ram and if you don't run dual drives and if they're slower drives.

ALSO...MSI motherboards have a trick you may have to do with the bios. We'll see how that goes first. Looks like decent specs. I was going to mention the SATA speed, but I don't know if it helps audio but can't hurt.

FYI, I typed a lot of this before I noticed you posted the new PC specs, but looks like you still might want to get another drive and clean install the OS on that one & use the big drive for audio ? Good luck