In contrast, the $125,000 is included in the $850,000, as indicated by the breakdown in the table on page 9. Thus, though not stated explicitly, the report indicates that the $125,000 was sent to MIT (to fund Seth Lloyd's research but not into his personal bank account).
(At any rate, the fact that he accepted a gift of any amount, especially into his personal bank account, is very concerning. Sounds like currently he has been put on administrative leave and we'll see what happens after they're done deciding what to do.)