I haven't seen any negative cost bases in my 1099 and I have close to 1500 transactions. You shouldn't have to manually change any values. Perhaps there are left over entries from your manual adjustments.
To test this out, start a fresh return and only import your 1099 and see if you still have the error. Also, you should be able to quickly browse thru your 1099 to see if you have actually have negative cost bases in any of the entries.
