With your SD card inserted, go to Menu > Settings > Applications > Manage applications > "Name of whatever navigation application that you're using here" > Clear cache.
If that doesn't work, you can try going to the same location, but tapping on, "Clear data," instead. It will most likely erase the settings for your navigation application, but at least there's a good chance that it will fix your problem.
If neither of the two options above work, connect your phone to your computer and browse the files on your SD card. Find the folder that is similarly named to the navigation application that you use, and delete it. Then try using the application again with the card inserted and unplugged from the computer.
Lastly, if all else fails, attempt a factory reset. I know this sounds harsh, but it's the last thing that I can think of right off the top of my head.
Please post back with your results, and good luck.