We don't actually look for text like "Out of Office". We look for a number of different headers set by Exchange, Lotus, and other email systems. We added some additional checks due to some changes in the way Exchange works in recent versions, and those new checks in ServiceDesk were released only last week.
The 'Ignore Out of Office emails' setting doesn't really do much. We still ignore conforming out of office emails when that is not checked. That setting sets up a different return-path which helps in some email server configurations.
If you have a specific example of it not working then the best thing to do is to contact Citrix Global Support with the Incident reference number in question. Then we can examine the email headers and figure out why we didn't pick it up.