When are two database objects equal? The answer is: it depends! It depends on what you want to compare those objects. For example: is "Equal" equal to "equal?" The comparison options allow you to have complete control over the comparison engine which considers those options before deciding to mark a pair of objects as equal or different.
So, when two object are found to be different by the comparison engine while you believe they should be equal, or they are found to be equal while you believe they should be different don't panic. Investigate the differences and carefully review the comparison options. More likely than not one of those options holds the answer to your surprise.
Please do note that some of the options, especially those listed on the advanced tab may be unknown to you depending on the level of familiarity with Oracle and it would have been helpful to provide a description for each. However, due to space and other restrictions, instead of us providing an incomplete and insufficient description that attempts to summarize information already available in the Oracle documentation we selected to omit those descriptions and let you consult the source directly when necessary.