This could be a bit hard to troubleshoot without seeing the actual file itself to get a better understanding of exactly what's going on.
As a first resort I might recommend trying to export your MySQL database in phpMyAdmin to a .sql file on your local machine, since it sounds like you're not having issues with importing the data as a CSV file there.
Then on our server you can try to import your MySQL database in phpMyAdmin with that .sql file.
If that doesn't do the trick for you, please send your database backups in to us at email@example.com as an attachment so that we can take a closer look at it for you. Please include the subject "Importing HTML into a MySQL database", and then respond back to this question once you've mailed it in so we know to go look for it.
I hope the first option works for you, but if not we'll try to get things squared away for you.
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