Parallel Port Dropping Steps

I've never posted to a forum before now. I usually beat my head against a wall until I figure it out myself but I'm not sure what's going on here.

The Problem
I've set up a new machine. Normal XYZ running version 2.8.1 with 2 PPort PCIe cards and BOBs. I ran Stepconf like I always do to set up an initial hal and ini file. I tested the steppers in Stepconf and they worked perfect. Smooth and precise motion. I launched my configuration and when I jog the machine though I get really jittery motion. What's also interesting though is that it worked perfect in stepconf, and if I issue a G0X.. (or G1) command in MDI it works perfect again. I opened up halscope to view the parport.0.pin-02-out (X step pin). When I jogged the X axis, it looks like the step pulses are getting dropped since there were intermittent gaps between pulses. When I issued the G0 command, the were no gaps (links to the pictures below).

What I've Tried
Setting step time and step space to 10000ns and 20000ns.
Setting the base thread to 50000ns in Stepconf and 150000ns manually in the ini file

Other Important Info
I don't think this is a hardware problem as it happens on all axes.
I'm not using the reset function as Stepconf doesn't add it in the hal file

Halscope snapshot jogging x axis:
photos.app.goo.gl/UzHY3ya4RpFAhFzT9

Halscope snapshot using G0 command with x axis:
photos.app.goo.gl/exc4XLomFfvZD6wS9

Here is the latest hal and ini file I've tried too.
Thanks in advance!

That fixed it. Thank you so much!