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@Gordon
I'll take a look at this in the next few hours. Seems strange though as it's basically the same chip as on the Pico (albeit with more memory and a higher clock speed) - about all I can think is the higher clock speed might be throwing off the PWM timings, but I'll check this.
The only other thing I can think is that the WiFi's timing is actually more accurate - because it has an external low speed oscillator. If you recorded the IR signal on the Pico then the WiFi might replay it at a very slightly different speed. There shouldn't be more than 2% in it, but I guess that could be enough.