GemCad typically does not lie. This cut works as shown, with the angles listed, but you may need to use a different process to get it right. This is not at all uncommon.
This design is the perfect example of the value of using the CAM method to cut a gem. CAM is “Centerpoint Angle Method” CAM for short. The sequence listed for this gem results in an estimated facet length when going from G1 to 2. It is not “meet-point” faceting friendly as shown. In order to cut this gem in 100% meet-point fashion, you would need to re-sequence (not the best way), or use a CAM preform.
If you learn to use the CAM preform, you will establish the exact girdle outline first, by using temporary center-point facets, which will be eventually, cut away. I use this method all the time, to avoid the situation you seem to be describing with your efforts. This does require you to use GemCad, or GemCutStudio, to create a CAM preform design first. I completely recommend this to everyone.
I suspect that when you cut your #2 tier, that you had to estimate your G1 length, which is inherently inaccurate, thus causing the angle issues you describe.
I hope this helps.