Just like Wine, Boxedwine won't work with games that have CD checks. If it is just trying to find the CD in order to play a video off of it or grab a large file it didn't install, that might work, but only if the code isn't making sure its a real CD device. Seems like my UI should be able to handle the user dragging an installer into it from a CD where the CD will be used again. For that to work it would need to copy the CD and mount it internally so that the program can find it again while running. Right now I don't do that, but I think that would be a useful enhancement that isn't too hard to do.
As for the Putt-Putt, that has the look of flash or Adobe Air. I know that things like Java, and .Net don't work yet in Boxedwine, so if it is doing any kind of JIT then it won't work. I added that to the list of games I should look at.
You got pretty unlucky if you only tried 2 older games like that and neither worked.
I did get them working and playable some time ago on Linux using Wine though (my little brother likes to play them still, except he can't get used to Linux), even though they ask for CD-rom.
The Putt-Putt game is using some custom click 'n play Python2 based "SCUMM" engine, it doesn't require Java or .NET iirc. And I think they predate JIT a bit.