For cube decisions and checker plays, I do the rollout by selecting from the analysis window, never the "hint" window, and never have problems with the rollout data not being saved when I save the file.
For a cube decision you can set up the position the same way as for a checker play, but then you can't (afaik) get rid of the dice roll, so the dice appear on the board in the middle of your cube decision.
So ... what I usually do is something like this:
If the cube decision position I want is this:
The score (after 0 games) is: Lars Trabolt 0, Masayuki Mochizuki 0
Move number 4: Masayuki Mochizuki on roll, cube decision?
| Lars Trabolt | 2 |
|---|---|
| |
| Masayuki Mochizuki | 7 |
Position ID: AwAAEAEAAAAAAA Match ID: cAkAAAAAAAAA | |
First I'll set up this:
The score (after 0 games) is: Lars Trabolt 0, Masayuki Mochizuki 0
Move number 3: Lars Trabolt to play 21
| Lars Trabolt | 4 |
|---|---|
| |
| Masayuki Mochizuki | 7 |
Position ID: IgAAeAAAAAAAAA Match ID: MAEFAAAAAAAA | |
and play the 2-1 to get to the position I want.
It's not perfectly unclunky, but it works.
I think my GNUBG wish list would include a command for "Create New Position," followed by prompts for setting the score, the cube position, the player on roll, and the player names, followed by a reminder to set the checkers where I want them and to turn off "edit" when I'm done.