The Fed is cutting its balance sheet and thus losing money [1]. (When the Fed wants to lower rates it buys bonds, thus raising their price. That creates accounting profits. When it wants to prop rates up it sells bonds; that depresses their price leading to accounting losses.)
The Fed isn’t pocketing change owed to the Treasury. It hasn’t properly owed anything on account of having shrunk its balance sheet by trillions of dollars [2].
There is zero evidence the Fed hasn't been paying the Treasury properly and a lot of audit evidence it has been.