I think you are on the right track to solving this problem. Let me give you my interpretation of the GPIB transceiver loading issue.
The maximum number of GPIB loads on any bus must be 15 or less. This is part of the original IEEE 488.1 specification. The reason for this is that each GPIB transceiver must be able to drive all of the other GPIB transceivers to a low logic state. GPIB transceivers implement a Thevenin voltage of about 3.3V when they are not driving the bus. So, when a transceiver wants to drive a particular signal low, it must drive it low while all the other transceivers are pulling it high. Limiting the number of other transceivers on the bus sets a limit as to how strong the drive strength of the GPIB driver must be. That is the reason for the maximum of 15 loads.
What may be happening in your case is that when you have 20 devices connected, there will be one transceiver driving a signal low while 19 transceivers are pulling the signal high. The driver may not be able to drive the signal low enough to be recognized as a logic 0.
The extenders do state the capability to extend the loading limit from 15 to 28 devices, but only on the same logical bus, not on the same physical bus. The limit of 15 devices per physical bus still exists even with the extenders. If you want to connect 20 devices on the same logical bus, you can connect 14 devices together and 1 end of the extender on the same physical bus. Then you can connect the other end of the extender to the remaining 6 devices on a separate physical. This would not violate the maximum of 15 loads per physical bus.
This is also where the device limit of 28 comes from. Each physical bus can have up to 15 loads. If you have 2 physical busses and one of the loads on each is an extender, that means 14 loads on each physical bus are left for devices, and the two different physical busses are combined to one logical bus by the extender. With a maximum of 14 devices on each of the physical busses, the device count is now 28 for the logical bus. The GPIB load count "starts over" across each extender because the extender is only one electrical load.
So, to answer your original question, can you divide your two physical busses such that there are not more than 15 devices per bus? For example, 8 loads on one side of the extender and 12 loads on the other side?