Hi Andrzej
Sorting arguments could be a good trick to bypass the problem. After finding the reason I have added sorting to my scripts and now it works OK.
I've created a patch (attached) that does the sorting. It will need some testing. I removed all the old code that attempted to fix up the sections after they had been created. It does seem that it was that code that caused the map source crashes. Jar file at: http://files.mkgmap.org.uk/download/294/mkgmap.jar
Differences in img files worry me a bit too. I can't see any negative consequences but it looks like compilation is state dependent, maybe some variables are not cleared at the start of new img?
This is harmless, files can always be different unless you give the --preserve-element-order option. A quick test shows no differences for me if that option is given. Cheers, ..Steve