Yes, reporting the
amount paid for the shares as the cost basis is incorrect for both qualifying and non-qualifying distributions.
See
Publication 525 for information about how the income from these shares is determined.
For a qualifying disposition, the difference between the price you paid and the fair market value on the
option grant date counts as compensation income on your W-2.
For a disqualifying disposition, the difference between the price you paid and the fair market value on the
purchase date counts as compensation income on your W-2.
In both cases, your cost basis should not be the price you paid for the shares, it should be the price you paid
plus this compensation income that is already reported on your W-2. Adjusting your cost basis upward by this amount prevents this compensation income piece from being doubly taxed as both compensation and a capital gain.