I noticed that when using different boards joined together , the units that are located in hexes that belong to both the boards are not displayed correctly and sometimes vanish. It seems that the system is not able to correctly determine the position of the units that are in these hexagons. Very often only some of them are displayed by Mouse Stack Viewer. Moving the units at the top of the stack, sometimes those that are below reappear, sometimes not.
The problem here is that you are ending up with two different stacks. One is the half-hex on one board, and the other is the half-hex on the other board. Since they snap to the center of the full hexagon, both stacks are in the same spot visually.
If you’re cutting up a map for easier handling, moving the cut away from hex centers generally alleviates the problem. If you’ve got two actual boards butting up against each other… well, everyone using VASL feels your pain. The best I’ve got is just be consistent as to where your cursor is when you drop the counters as that’s what picks which half-hex you’re in.