I've just noticed, when you run the game through Steam it will load a different savegame than if you launch it directly. This can lead to "desynchronized" saves if you launch the game through Steam, play, then launch directly.
Hi Image Not Available (nice nick by the way ), this is the defined behaviour right now. If run through Steam, saves are stored as Steam Cloud files. If you launch directly, it behaves as the "DRM free" version and saves in the Halfway folder. We've had ideas to synchronise saves between versions, but this isn't trivial, requires versioning of some sort, and needs to be robust enough to prevent data loss.
Ah, in that case its probably for the better, as a fellow programmer I can empathize. Your attention is better spend on making the actual game better (something you've done a pretty good job off so far).