I have quicken installed on Ubuntu 11.
I have found only two issues and both are graphics related.
The icon graphics are off color and pixelated. It reminds me of what Windows looks like before you install a graphics driver. This is a minor glitch and doesn't affect the functionality of the program.
The second issue is that when entering data into a register entry if a popup window is activated it doesn't retract when you move on to another entry block. This creates overlapping windows that make reading the entry difficult. The current popup is always on top so it doesn't directly impede data entry. All the popups close when you move to a new entry.