no need to change the differential oil 3 times in 5000klms!! I doubt it would affect the gear change anyhow, unless its the WRONG oil specification.
A few owners had problems selecting 5th and 6 th when the CT was new but the problem seems to go away with more klms. Make sure you have the correct specification Engine oil (as per the handbook), it is much more likely to cause these problems.
Let us know.