has anyone come across penny rounding issues in NetSuite with Tax we are having issues where Shopify is rounding up by pennies

Yes, we had this issue, We have Celigo posting the tax amount, and then it somehow calculates a "rate" that rounds to the same amount charged. We found that Shopify was rounding the City, State, County tax separately. Then adding them together. This did match how Avalara does it. But slightly different then how NetSuite was trying to do it.

I had this issue once. We had to install avalara on the Shopify account to make both platforms match.