It appears as if no transfers were made to custom envelopes from income split, even though custom envelopes rules are set appropriately. I tried disabling and renabling autopilot which did not move funds between the custom envelopes.
This was not an issue until the hard spending limit feature was added. I assume it has something to do with the transfer to vault of remainder of daily budget, I.e. no transfer to custom autonomous envelopes happens until the remainder of the cash envelope is transferred to vault. But once that happens, there is no money in the cash account.
Another possibilty is that they are being considered manual envelopes even though they still possess the properties of an autonomous envelope. When opening the custom envelope settings, I am able to set the rules for autopilot. However, when I go to transfer cash out of the cash envelope, the autonomous envelopes are displayed as manual envelopes, separate from the default autonomous ones (cash, vault, etc).
Additionally, there is no way to view autopilot transactions for custom envelopes.