By default, TrueCrypt doesn't change the modification timestamp (shown in Windows as Date modified) of TrueCrypt containers when you change the files inside them. This is good when you want plausible deniability; the ability to claim, "look, I haven't touched that file in 3 years!". Unfortunately, it has the downside of breaking backup programs that use the last modified date to determine which files need to be backed up.
Luckily, you can change this behavior. In TrueCrypt, you can open Edit > Preferences, and uncheck Preserve modification time of file containers (see my post TrueCrypt timestamps). This setting is included in the release notes for Truecrypt 4.3a.
I found out the hard way that this setting doesn't apply to a TrueCrypt Traveler Disk. Because the Traveler Disk launches TrueCrypt using the Windows Autorun feature, it takes its marching orders from whatever parameters are passed in the autorun.inf file on the Traveler Disk, regardless of what you set in the Preferences. So, to turn off timestamp preservation, you need to add this parameter for TrueCrypt.exe in the autorun.inf file:
The file probably already has /m rm, so right behind it add /m ts. This is the command line parameter for "Do not preserve container modification timestamp". See the TrueCrypt Command Line Usage page for this and other parameters.