So:

1. You had a bitcoin wallet.dat running on windows with password #1,
2. you copy the Bitcoin wallet to an Ubuntu machine,
3. on the Ubuntu machine you change the password to password #2,
4. you are surprised that when you boot back into Windows and the password is still #1?

before starting anything: re-backup your windows wallet.dat to a different media (USB stick, encrypted 7zip with a strong password and email it to your gmail, etc.)

If you think you will be happy only using Ubuntu, you can migrate your day-to-day Bitcoin to that, which will be less likely to pick up viruses and spyware. You'll want to install Ubuntu on your computer, running off a live CD is inconvenient and it's storage of persistent data is capricious. The best way would be to use a fresh install of Bitcoin on the new Ubuntu (remove the .bitcoin directory and start again), which will give you a new wallet and new addresses, then close that Bitcoin and back up the new Ubuntu wallet.dat to a USB stick and store it safely. Then send all your Windows bitcoins to an address in the new wallet. Then even if someone has compromised the old install or stolen your old wallet, they will have no access to your Bitcoins.