I wanted to circle back on this in case someone is having a similar issue. We think that the trouble here is the way that the Jira New issue trigger looks for new information.
The Jira Software Cloud trigger looks for new issues every few minutes and we get the top 50 results, sorted by newest to oldest in terms of their creation date. If there are more than 50 issues that meet the parameters, then the older ones wont be ‘seen’ and trigger the Zap. We think the issue with this not catching all of the Issues in Jira is probably that maximum of 50 results.
In this case, the workaround was to switch to the trigger ‘Updated issue’ rather than ‘New Issue’ and to then use a filter step in the Zap to only continue if the issue met specific criteria.