There seems to be a delay in associating a new munchkin ID to a lead object. Here's the step-by-step breakdown:
This latency seems to fluctuate through out the day. The timing of the API calls we make is crucial. Is there any way to work around this or do we just have to retry?
Munchkin lead association is asynchronous, yes. This is expected behavior. Although it can appear synchronous in periods of low utilization, that's coincidental.
Where are you running the API call from? I hope you're not calling (or passthrough proxying) the API method directly from the browser.
I think you should describe your goals in detail (rather than just the current implementation)... immediately retrieving the Marketo ID _on the client_ is not a typical requirement.