There are some strange things about your original post.
1. First of all and number one. No programmer has the facility to control the pump overrun. So you cannot blame the LP722 device for this problem. Not all boilers require a pump overrun, so, when one is required, the pump and the overrun cycle are controlled by the boiler. The pump is connected to wiring terminals provided by the boiler manufacturer and so has no connection to the programmer.
2. Drayton programmers have the same wiring connections, they are only on & off switches for the heating and hot water functions and simply plug into the backplate without any changes to the wiring being required. So the wiring shouldn't have been touched.
3. As you have an 'S Plan' system, when the two motorised valves close because the heating and hot water are both satisfied, there needs to be another open circuit during overrun to allow the water to circulate around. This is known as a 'by-pass'.
The boiler by-pass is there to dissipate residual heat from the boiler when it goes off. If there is no flow of water around a by-pass and water stops circulating it will overheat and cause the sounds you describe, but it would normally also activate the overheat thermostat, which on the Baxi's I have seen, has to be reset manually. You don't mention this happening.
There are two types of by-pass, 'manual' which is basically a manually operated gate valve that is only partially open to maintain the minimal flow required by the boiler during overrun, and the 'automatic' type which when correctly calibrated adjust the flow rate automatically as and when required.
So, if it worked OK before the LP722 was installed, and the fault appeared at the same time, then something else was also changed. For example was a single 3 Port motorised valve replaced with the two 2 Port valves? Has the by-pass valve setting been tampered with? Was the wiring at the boiler changed?
So here is what I would do.
1. Check to see if the pump is still powered or not during the overrun cycle. [I assume here that the pump is working OK when the heating or hot water is operating]
2. If the pump wiring is correct, but the pump isn't overrunning, check there a permanent live supply to the boiler? If it has worked previously there will have been one at sometime. Has it been tampered with?
3. If the boiler wiring is correct and the pump doesn't overrun, then the boiler PCB is the most likely cause of the problem. It's quite easy for someone competent to check with a multimeter to see whether the boiler is providing the pump overrun control power.
4. If the pump is running, and the water is not circulating, find the by-pass valve and check that it has not been inadvertently closed down too much. In my mind this would probably be the most likely scenario, in that there is sufficient flow to prevent the overheat tripping, but not enough to stop the boiler noises.
you need to elaborate