Difficulty tracking down latency on new install

Hey everyone! Sorry for yet another latency post. I've spent a few hours every day for the last two weeks or so trying to troubleshoot my latency numbers, but I haven't been able to track down anything yet.

Running the latency test and moving things around with glxgears running, the numbers aren't fantastic at 40k ish but when I minimize a terminal window and then pull it back up, the latency jumps up to 200k or more. I've been able to quickly click around and minimize/maximize screens and had it up close to 400k which is pretty terrible (I just saw 372k max jitter servo and 381k max jitter base).

This is a pc I picked up off Craigslist. It came with ubuntu 16.04 running on it. I partitioned the drive and put debian wheezy with linuxcnc on it. Specs are:
Processor - Intel Pentium 4 2.53Ghz
System bus speed 533Mhz
System memory speed 333Mhz
Cache RAM 512kb
Motherboard is an Intel D845PEBT2
1gb ram
250g sata hard drive

I read through the motherboard spec and all bios settings and a lot of the power saving features don't exist and it's not multicore. I've gone through trying just about everything I can find online with enabling/disabling what I have available in bios without any appreciable change in numbers. I don't see periodic jitter changes so it shouldn't be the SMII issue. When I use the social command I see that the vga compatible controller is NVIDIA Corporation NV25 [GeForce4 Ti 4200] but I also know that the driver in use is the nouveau one...

Any thoughts? If latency jumps when I'm minimizing windows and then pulling them back up, is that a caching thing? Or video driver thing?

I'm brand new to Linux, so I've been enjoying learning as I go, but it's also been a bit of a headache. I have some stepper motors and a hobbycnc controller ready to go for my mill in my basement, I'm just trying to make sure this pc can handle it. There's nothing in the pc specs that suggests it should be a problem, so either I'm missing something or maybe there's some power saving bios type settings that aren't available to me. Oh and I should mention that I did create a live cd and try out an older version of linuxcnc with Ubuntu 8.04 but my latency numbers stayed the same.

Any thoughts or suggestions would really be appreciated. If it helps I can take some screenshots of the bios menus to show you what I have available to change.

Thanks!
Gavin

Thanks for the suggestion. I think I might have some RAM lying around I can try. You are correct that it's just DDR in there right now. I'll take a look at the fan too.

You mentioned hyperthreading... I was under the impression that it was a bios option. Is that correct? I didn't see a setting for that in my bios options. Also what's A20?

Thanks,
Gavin