Your strain MAY be undergoing "genome renewal".
Bob Mortimer et al. published a paper about this phenomenon in Yeast
10:1543-1552 ( 1994). The genome renewal phenomenon occured in several
Saccharomyces strains that they had isolated from fermenting grape
musts. These diploid strains changed from being heterozygous at
multiple loci to complete homozygotes. Perhaps there is a similar thing
occuring in your strain. Is the strain hapolid or diploid, how well
characterized is it? Maybe they sent you the wrong strain? Good luck!
sgd4 at pantheon.yale.edu