Ever since I switched from using DSLRDashboard to using my Timelapse+ intervalometer, I have been having some issues with LRT holy grail workflow.
1. 2* and 3* key frames are not matched. There is an exposure difference even after
running through the correct workflow.
2. For some reason, the ending single * keyframe is always blown out, even though it
did not look that way in the original picture file.
3. Unrelated issue? when I load my images into Lightroom,
the metadata/white balance seems to automatically change? As far as I know, there are no pre sets active in Lr to cause this.

I will post some images of these issues. I am no pro at either of these programs, but I'm hoping someone can help. Thank You in advance.

1) If Timelapse+ uses Bulbramping, the sequences might not be correctly processed in LRTimelapse. I'd suggest using qDslrDashboard. I've no experience with TL+, so I can't help, sorry.
2) That might be due to the Holy Grail Wizard, you might have to rotate the yellow curve appropriately.
3) That's normal, when initializing LRT sets the WB to a default value because it cannot read the "As shot" value from the files.
Just set the WB back to "As shot" or any other value when editing the keyframes.