I think what might be at play here is that the Split window is rendering off-screen.
When invoked, the Split window takes focus from the main Moneydance window and requires user-interaction to return said focus. e.g. clicking the 'Done' button.
Without the ability to provide the required Split window interaction, Moneydance will appear to have frozen.
Open Moneydance, create a new transaction and invoke the Split window. (Moneydance will appear to have frozen)
Use key-combo ALT-SPACEBAR (a small context menu may or may not appear at the edge of your monitor)
Tap the letter 'm' on your keyboard to invoke the 'Move' command.
Using your keyboard's ARROW keys, hold down the appropriate ARROW key (likely the LEFT ARROW key) to hopefully move the orphaned window back on-screen.
This phenomenon is usually caused by installing a second monitor to your machine and subsequently removing it.