Compatibility issues is not something I've seen. The whiteboards we use (Hitachi Starboards at our end, some Sharp at one of the other locations, and I'm not sure about the rest of the company) are input devices, windows treats them as a tablet device nothing more. They are glorified projectors with pen input.
Any collaboration software which will allow shared drawing on a single canvas works on these boards. Sure you get extra features if you use a specific manufacturer's own software like quick changing colours by tapping the side of the board, but ultimately that's minor and you may even get better features by not using their software.
Ultimately though the compatibility issue shouldn't really come into play at all since we are talking about one company with distributed teams. I would be very surprised if they don't standardize on a common vendor anyway.