When playing a position from the scratch board against an engine, the PGN isn't saved correctly:
1. The "SetUp" tag should be used when the starting position isn't a normal starting position for saved variant** (In this case, just about any position from the scratch board).
2. When the first move is made by Black, eboard doesn't add the "..." required for a Black first move***, using only a single period, as if it were a White first move.
I'll also note that the engine bookmarks ignore the color stated for the engine - the engine simply plays for the side whose move it is.