Why is the Federal ITC amount less than the ITC's percentage of the gross price?

The reason that your Federal ITC amount could be less than ITC's percentage of the gross customer price is that the tax credit basis has been modified by other incentives. The ITC percentage is multiplied by the "basis", which starts at the contract price.

However, the Federal ITC basis is affected when the customer receives a rebate on which they do not pay income tax. If you configure a rebate to be collected by the customer and do not mark it as taxable, that rebate amount will be subtracted from the gross price to obtain the Federal ITC's basis. Essentially the government is not going to double pay you. If the cost of the system is offset by another incentive, you cannot claim a tax credit on that free money.

SolarNexus strongly recommends collecting rebates on behalf of the customer, or marking all rebates as taxable. Typically paying income tax on a rebate is significantly less than losing that portion of the Federal tax credit.

If you've found this issue with an existing solution, mark the incentive as taxable, and then re-run the analysis. You will then get the full tax credit basis, but a tax liability on the rebate. That's still typically advantageous to the customer.