I suppose wine on Ubuntu has the same structure of directory like Debian.
Try this.
Change name /home/user/.wine to /home/user/.wine2
Run wineboot
Create on the new /home/user/.wine/drive_c/Program Files/Perpetuum/
and copy the game files inside.
Reinstall d3dx9 with winetricks.
And try to run into a terminal "wine Perpetuum.exe".
If dont run, you can see errors on the terminal.

Is a wine system flush to see if perpetuum works. I have encountered a lot of problems between a lot of installs on same system.
To restore your previous install move .wine and restore .wine2 to .wine

PD: Sorry, my english sux, I know