Well, as the tree said to the lumberjack...
Opened up that last project and sure enough everything is assigned properly pin wise, but symbols are definitely inconsistent between schematic and board. Standard Designspark diodes work as they should though when I added them as a test, while the original Modelsource ones are messed up.
So out of curiosity I started a new project and added default Designspark diodes as well as the same Modelsource diodes used in the other project. Works fricken perfectly. Maybe I'm going crazy, or it's user error, right? So I open the original project back up and delete the traces to the diodes in question to see if I've somehow manually routed wrong (I know I didn't, because I remember majorly getting the shits about the symbols when I was routing and posting this rant, but let's assume I'm an idiot and messed up). Nope, the thing is still telling me to route them backwards. There is definitely something wrong here.
Ahh, the joys of software.