Lucas,
D&C Manager should not draw two identical chains differently if the same D&C Manager item is used to plot the chain. To determine if this is what is happening in your case, I would need the D&C Manager database that you are using, the item you are selecting and your gpk file. If you will send me those files I would be happy to look at what is happening.
Lucas - I was able to reproduce what you are seeing, but D&C manager seems to be visualizing like it should. I've attached my dgn with the results.
Here is what I did:
Chain1 -- Store point 101, then stored point 102 by traverse 300.0000001 feet due north. Store Chain1 from points 101 & 102.
Chain2 -- Store point 201, then stored point 202 by traverse 300.000000 feet due north. Store Chain2 from points 201 & 202.
When I visualized the chains and stationing using D&C Manager, Chain1 shows Sta. 10+00 due to the fact that the chain extends ever so slightly beyond it. Chain2 ends exactly at 10+00, so it doesn't show.
Could this be what you are experiencing?