This article has very limited use case. If you are:

• Using additional JQL restriction in you context configuration
• Do not use "Create Remote" button
• Your JQL is being met for an issue on the same event, which initiates synchronization (CREATE). For example ISSUE_CREATED event.

Issue within such a initial synchronization is that issue is not being found as valid for synchronization (JQL), because it has not been yet reindexed. It will be in a second or two. 
This is why we have a simple workaround, which just delays your JQL verification for configured amount of time (seconds). Such a time may vary on your instance performance and size. 

In jira-config.properties add a line, where number is a time in seconds:

issuesync.create.event.delay=2

Only contexts with JQL present will be affected with such a delay.