MXF is only a wrapper to the codec, so when you say “transcode to MXF” it can either be rewrapping the codec as MXF (a consolidate) which now becomes Avid managed versus AMA linked, or it might also include a transcode to an MAXF wrapped DNxHD codec. There are two things to look at here – when you transcode are you selecting an equivalent DNxHD codec data rate wise? If so, the issue might be the overhead that AMA imposes, so perhaps trying a consolidate (rewrap only) of the ProRes codec might be the answer. If you are transcoding to a smaller data rate DNxHD, then it is a throughput issue with either drive speed, drive connection, drive type, etc.
Michael