Hi
There are a few files which are overlapping in the list that you show, this will explain why some files get overwritten when you copy them.
The reason why the mmch.js file is being cut is becasue the file system doesn't have enough space for it to fit (there is space for a about 40k from location 'Y' and the file is about 52k).
But it looks as though your are almost there. I suggest that you make a copy of the following file
\Applications\uTaskerV1.3\WebPages\WebPagesM5223X\FileSystem\FileSystemM5223X_160k.doc
Then adjust it to suit your length (you are defining a file system size of 128k, starting at 64k in FLASH, so you can increase the size as the M52233 has 256k in total - note that your application may grow, so it may be an idea to start the file system higher in memory. Don't forget that the project supports the file system in cheap external SPI FLASH if memory does become a problem).
Then you can mark in your files and their sizes. You will see for instance that your files ejc.htm and md.jpg are presently overlapping. The second one which is copied will need to delete the first one to make space for itself...
It also looks like mmch.css (if it is really 18k in size) is also overlapping with several other files.
After making a few changes to ensure that the files respect the uFileSystem naming conventions you should then find that it works correctly.
regards
Mark