Err thinking about it just now, if it was with the generic install-sh or some other approach, I bet it's because the install script doesn't remove the old contents and so PTS went from having a downloads.xml file for that test to having none, since everything is all generated now for it on the fly. So if you just rm that downloads.xml file within pts/test-resources/compress-gzip/ it should fix that.
Where is the pts folder located? or do you mean .phoronix-test-suite/test-ressources in the home dir from where the test was run from? Because I created the user pts just the other day and that home dir has never had another version of PTS. I used to run from root simply because i didn't want to create a nis user and the files where too big for the NFS share and symbolically linking them would cause obvious problems on other boxes.