What version of Videopad is being used? Try this one and see if the issue persists. Ignore any virus warnings.
One method in VP...
Select all the overdriven mp3s, then click the FX icon on one of them.
Choose Amplify, make the change, and close the box.
Click on the FX of the clip that was changed and in the tool menu click the left FX button... 
The change that you made will be applied to all selected clips.
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Wavepad can do batch conversion for mp3s.
Open the 3-lined Menu, then TOOLS | Batch Converter. Add the files.
In step 2, click on ADD EFFECT. Scroll down and choose Amplify. Or try Normalize. Then use the converted files in Videopad.

For more info on Wavepad, check into the forum.