I was researching the issue you are describing and had a recommendation. The device is very simple, so the software troubleshooting for it is pretty limitted so I think you shoud restore the iPod shuffle and re sync the content. That way, if it is a software issue, this will fix it. Here is the article named Restoring iPod shuffle to factory settings found here: http://support.apple.com/kb/HT1481.
It is important to understand the difference between "update" and "restore." Update does not affect your settings or songs, it simply installs updated software that controls iPod shuffle. Restore erases the disk and restores iPod shuffle to its original factory condition with updated software. If you only need to update iPod shuffle, this should be done on the computer where music is normally synced. Updating on another computer will result in all songs being removed from iPod shuffle.
Warning: Because Restore erases all songs and files on iPod shuffle, make sure to back up any files you've saved on iPod shuffle. Your songs, podcasts, and audiobooks can be synced back to your iPod shuffle if the items are part of your iTunes library.
How to restore iPod shuffle
- Ensure that you have an active Internet connection as new versions of iTunes and iPod Software may need to be downloaded to your computer.
- Download and install the latest version of iTunes if you do not already have it installed.
- Open iTunes, and then connect iPod shuffle to your computer.
- After a few moments, iPod shuffle will appear in the Devices section on the left side of the Tunes window.
- Select iPod shuffle under Devices and you will see information about it appear in the main iTunes window under the Summary tab/button for iPod shuffle (3rd and 4th generation) or the Settings tab/button for iPod shuffle (1st or 2nd generation).
- The Version section tells you whether iPod shuffle is up to date or needs a newer version of the software.
- Click the Restore button. You will be presented with one or more restore options that may prompt iTunes to automatically download the latest iPod Software. The 4-possible restore options are:
- Restore Option 1: Restore - Restores with same iPod Software version already on iPod.
- Restore Option 2: Use Same Version - Restores with same iPod Software version already on iPod even though a newer version is available.
- Restore Option 3: Use Newest Version - Restores with the latest iPod Software currently on your computer.
- Restore Option 4: Restore and Update - Restores after downloading the latest iPod Software on your computer.
- If you are using a Mac, a message will appear prompting you to enter an administrator’s name and password.
- A progress indicator will appear on the computer screen indicating that the restore process has started. Do not disconnect iPod shuffle during the restore process.
- After the restore process is complete, the iPod shuffle's status light will flash orange continuously. The iPod Setup Assistant window will appear asking you to name your iPod and choose your syncing preferences as you did when you connected your iPod shuffle for the first time.
When you come to step 7, I recommend Restore Option 4.