K, last bit of info after some more tests :

For the record a 'du' still shows the file sizes as identical, ie the file for the compressed table isn't sparse. I realise now the directory listing I posted above wasn't a good indication of success.

For comparison I have installed and run the same test with Mysql 5.7 with page compressions, and can see the file sizes reported the same by ls, but they are taking up less space when looking at them with du (about half the size)
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Could this problem be because 'innodb_use_trim' is disabled? If I emable it the server crashes and also seems to corrupt the db, sample info for this below :