Hello Daniel,
I looked at the output of your screenshot, and tried to look for some of those directories.
And, for example, mine installation of MQX 4.2 does not even have mqx/source/bsp/twrmcf52259 (second line on your screenshot), and similarly for next one I checked.
I'm curious which installation of 4.2 MQX you used. Once difference I see it seems a Windows install.
But must be something else, could be we have totally different install files?
I believe I used these - Linux base & applied the patches