I have also synthesized Ti3AlC2 and observing differences in the intensity peak of XRD, even after controlling the rpm and duration of my ball milling.
Although ball milling is very good to make the homogeneous alloy. Ofcourse with said RPM and duration is good enough and hope you have used in recommended way. Another most important parameter is the ball to sample ratio. I mean stainless ball or zirconia ball using during milling. In addition to this, if the alloy is not formed completely the phase will be different and thus you might notice the peak position and intensity different than the report. Carefully check each parameter, if everything is fine I recommend to repeat the milling with slight change in duration i.e. longer duration and hope you will get the right track.
One most important point I missed to say is the scan time and rotation of sample holder while making powder xrd measurements. If you do not use enough time i.e. slow scan of xrd pattern, you might get low intensity. If the measurements is carried on the static sample holder without rotation, you can get preffered orientation effect which also alter the intensity ratio. In usual lab xrd you can minimise the preffered orientation by rotation of sample holder but can not remove completely. For a better xrd data without preffered orientation contribution, I recommend to use the synchrotron measurements. You will get high signal to noise ratio. Hope this will help you to plan your experiment.
Check the Ball to Powder ratio. Greater the ball to powder ratio only increases the collision frequency. This decreases the time it takes for the powders to evolve.
Actually I am not getting your point. Are you getting different position or intensity. If you are getting change in intensity the it may be because of instrument you are using. If peak position itself different then may be you have impurities in your sample.