Yes, as long as the files do not exceed the limits imposed by Music Creator.
There should be no difference between MIDI files created by any Cakewalk DAW. Music Creator shares the same code base as SONAR. The latest version of Music Creator is based on the original code for the new SONAR. MC6T was based on X2a.
You best solution would be to provide more details about one or more (but I would suggest working on one at a time) of your systems, the issues encountered and get them working properly with SONAR instead of falling back to Music Creator.