Hi Jan, the difference between 5.5.0063 and 5.5.0066 is just a few bugfixes. However, unfortunately one of them introduced a new bug to 5.5.0066 which has been fixed in the later versions. Could you please upgrade to the latest version (currently 5.5.0070) from http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_stable/ That should fix the problem (please let us know if it does not)
Pavol.