only part of carry-forward clean energy credit is applied to amount owed.

The credit can't be more than your tax liability.  Your tax liability is what the IRS keep at the end of everything; if you had $5000 of withholding and a $1000 refund, your liability was $4000.  If you have withholding of $3000 and owe $1000 more, you still have a liability of $4000. 

Your tax liability might be significantly reduced by something like the child tax credit or other credits.  Also, the energy credit can only count against income taxes, it does not count against self-employment taxes or any penalties (such as from IRA withdrawals etc.)

Print out a copy of your tax return and check lines 16-22.  If you are getting the maximum credit this year, line 22 will be zero.  If line 22 is not zero, then there may be a problem with the credit and you would have to call customer service.