OK, got it working:-) All the powerpacker decompresses claimed blind that those files were not compressed. So I went back to a trick suggested by some people on newsgroups.
The trick was to run Civ from disks. Then exit to DOS. From the cli copy the contents of all the disks to HDD. This decompresses them on the copy since Civ has installed a system patch to decompress files on reading. Though I still had to use xfddecrunch to decrunch the CivilizationAGA binary itself, oddly.
Now the question is - why does the decrunch of the other files work for everyone else? What is it about my box? I tried uae as well with the same results...
Mark