not sure how far you have gone in MyHarmony interface (yes, it's a nightmare probably designed by a maze architect for alien civilizations), you may know it all already, but there are a few parameters which may lead to the situation you are describing. Each one is "device specific":
- inter key delay: the minimal time between 2 signals, usually 100ms.
- repeat value: corresponds approximately to the "duration of each signal", value between 0 and 3
- power-on readyness: after power-on signal, time before send the next signal, usually 1000 to 4000ms
- input readyness: after changing the input canal of the device, time before send the next signal, usually 500ms
- delay between devices: don't know where to configure this one, but Logitech is describing it as: "each IR signal is received and treated by each device, and ignored if not relevant to the device. After receiving a signal, some devices enter in an analyzing and treating delay, and don't accept furthermore signal during this lapse of time." I think there is a delay added between 2 signals to different devices.
All these can make a sequence very long, according to the various devices involved.
By experience, you can often reduce the inter key delay to 0ms, which decreases drastically the overall delay of a sequence.