Just for a laugh I chopped out the Verilog version of the Instructor Pointer board and hooked up the real IP board. With a logic analyzer connected to the interface between the two I triggered the recording on the falling edge of the Power-On Clear output. At first I got garbage, then realized that the soft reset was far too short to clear the real IP DRAM array. Holding the POC input button I reset the analyzer's trigger, held my breath, and released the reset.
During the first machine cycle the hardware IP board reports an address of 000 (hex) at the appropriate time, which is correct. The soft 4001 ROM responds with 00 (hex) — a NOP instruction — which is also correct. So far, so good. During the second machine cycle the IP board reports an address of 001h, which suggests that the incrementer circuit is working. The soft ROM responds with another NOP, again correct.
The third cycle produces address 002h, more evidence of a successful increment. The instruction fetched is 40h — a JUN, or unconditional jump, a two-cycle instruction — again correct, and the JUN+JMS and SC signals from the soft instruction decoder switch states at the proper time. The fourth cycle produces address 003h and the byte fetched is 0Bh, the proper destination address for the jump. What should happen here is that, instead of incrementing the current IP value, the IP board should store the destination address of 0Bh. This apparently is not happening properly, as the next address to come out is F0Fh. From there it goes F10h, which is wrong but makes sense, 101h, which doesn't, and downhill from there.
The signals being fed into the IP board look roughly correct, based on the both simulators' outputs. The problem appears to be fairly repeatable, which will make it easier to debug. In fact, it's so repeatable I suspect the problem is that the soft 4001 ROM isn't outputting the data long enough to meet timing with the real IP board. If this isn't it I may have to probe some internal signals, which will necessitate soldering some wire loops to the board to form test points I can grab with a micro-clip.
Unfortunately I don't have time to dig into the problem further tonight.