You have to ask yourself which directory you are in at the time you execute the xlsread() and the other statements. In a compiled executable, chances are that you are in ctfroot() and that all action is taking place there.
If the original counter.xlsx is saved as part of the compiled executable, then each time the executable were re-expanded then the file would get overwritten.
You should probably be considering detecting the directories already present instead of relying on a counter like that. Detecting directories would be a little easier if you used zero-padded counters, such as Problem_00018 instead of Problem_18 . For that,
newdir = sprintf('Problem_%05d', c);
I note that you are using movefile(): if those worked, then the files would not be there for a second execution. Perhaps you should be using copyfile() ?
