Do ANY of those tax rates ACTUALLY apply to things YOU are registered to collect and remit tax for? Or are they just a huge list of POSSIBLE tax rates that one MIGHT use, and were forced upon you by a default Magento install?

ie: do you know what each of those rates is there for, and do each of them actually apply to your business?
If not, why not wipe them out and set up just the rates that YOU actually need?

If they ARE *all* required by your store, then you'll need to rework how they're used, and set up all the required geo_zones records to match each of the tax_zones you've got in that table. Right now you're likely getting it applying all taxes on top of each other regardless of zone because you probably don't actually have matching geo-zones for any of them. Just a hunch.