The outputs of Misha will always be gates, the length will be determined by how long you press/hold the interval button or the short/med/long setting.
The inputs can be configured to be either triggers or gate/cv pairs, with a long list of options to customize how these work.
Your hypothesis may be correct, in the setup you are using the signal is mostly high and only goes low for a brief moment, so that may be throwing off your envelope generator.
