A new USPTO fee schedule took effect on January 16, 2018, which usually means that all fees must be paid at the new (higher) rate. However, thanks to revisions to 35 USC § 151 effected by the Patent Law Treaties Implementation Act of 2012, applicants paying an Issue Fee need only pay the amount set forth on the Notice of Allowance.
As noted above, the statute at issue is 35 USC § 151 . As amended by the PLTIA, that statute provides:
35 U.S.C. 151 ISSUE OF PATENT.
(a) IN GENERAL.—If it appears that an applicant is entitled to a patent under the law, a written notice of allowance of the application shall be given or mailed to the applicant. The notice shall specify a sum, constituting the issue fee and any required publication fee, which shall be paid within 3 months thereafter.
(b) EFFECT OF PAYMENT.—Upon payment of this sum the patent may issue, but if payment is not timely made, the application shall be regarded as abandoned.
As the USPTO explained in the corresponding Federal Register Notice:
Under the changes to 35 USC § 151 in the PLTIA, the sum specified in the notice of allowance will constitute the issue fee and any required publication fee, and the Office will proceed to issue a patent when the applicant pays the sum specified in the notice of allowance, regardless of the issue fee and/or publication fee in effect on the date the sum specified in the notice of allowance is paid.
This means that large entities do not have to pay Issue Fees at the current ($40 higher) rate until they are paying fees pursuant to a notice of allowance that sets forth the higher amount ($1000). Anecdotally, I received a notice of allowance issued January 16, 2018 that still set forth the lower fee.
Please see this article for a discussion of other significant changes effected under the Patent Law Treaty.