The direct rollover from the 401(k) to a traditional IRA is not taxable. You can see this by seeing that everything in column B of Form 10401-X is zero.
Any refund or balance due shown when you prepare Form 1040-X is in addition to what was shown on your original return. The refund shown on your original return is still paid.
The only reason to file Form 1040-X under this situation is to provide explanation that the rollover was actually completed and that it results in no change in tax liability. Had you included it on your original tax return the only effect would have been to have included it on Form 1040 line 5a, exclude it from line 5b and include the word ROLLOVER next to line 5b.
