Which system has the bootloader in the master boot record? I'm not sure how Grub4DOS fits into this whole equation. Puppy still AFAIK still uses Grub Legacy and Ubuntu uses Grub2. Do you have a separate boot partition where you have Grub4DOS or did you install it on one of the partitions?
Maybe we can get a little clarification if you go to the site below, read the instructions, download and run the bootinfoscript from either Ubuntu or Puppy and post the output here, a results.txt page.