When you export (in5 > Export HTML5 with in5...), you can set the background in the Backgrounds section of the export dialog. You could try going there to reset the Background color to Default.
I would also recommend checking that you have the most recent version of in5 which is 3.8.7.
If you're still not getting the desired result after resetting the background color and/or updating to the most recent version, would you be able to send us your InDesign file or a sample file that recreates the issue and your html5_output folder? You can send it to