security concerns in dual-boot Linux, Windows system?

Solution 1:

Darn near impossible (or at least impractical). The proportion of computer users who dual-boot Windows/Linux is so small that it's not worth anyone's time to write the code required to access a Linux partition from Vista and corrupt it. And it would have to be done intentionally; I'm sure it's safe to say that Windows will not have a major bug in the filesystem code that wreaks havoc on the HD with complete disregard for partition boundaries.

So what I'm saying, in less-than-eloquent terms, is not to worry about it. At all. (Unless you install a driver to access your Linux partition(s) from Windows, then, you might want to worry just a little bit.)

Solution 2:

The major threat is here to install Windows after Linux. You might loose the boot-loader. Check RecoveringUbuntuAfterInstallingWindows on Ubuntu's wiki.

Now, regarding malicious code, David answered very well.