First, I'd recommend checking that you're using the latest version of in5. The current version is v3.8.6. Check your version by going to in5 > Info and Updates... and checking the version number in the upper right of the in5 - Info & Updates dialog that opens. If it's an earlier version, try downloading the latest version, installing it, and re-exporting your content.
If you're still having issues after updating to the latest version, would you be able to send us your InDesign file (or a sample file that recreates the issue) and your html5_output for us to troubleshoot? You can send it to: