Why is my transmission shifting inconsistently

Although most modern cars have separate computers that control the engine and transmission, there is a lot of crossover between them, so it's fairly likely that whatever is causing your late shifting may be reported by the engine computer in the form a Diagnostic Trouble Code (DTC) that can be read from the engine computer via the On-Board Diagnostics (OBD-II) port in your Jeep. The check engine light is saying that your rig has a problem to report, so it would be a good first step to find out what it's trying to tell you.

You can pick up a bluetooth adapter that'll connect up to an app on your phone to read the codes for under $10 USD and you can get several free apps (Torque is a popular one) that will pull the codes for you. Alternatively, if you take it to an auto parts store, most of them (at least here in the US) will hook up their OBD-II scanners for free and give you a report on the trouble codes.

Once you have a list of your code or codes, come on back and tell us what you found and we'll have a much better idea of what to tell you regarding why your transmission is being flaky. Also, it'll be a big help if you tell us what year and engine you've got in your rig.