Ref: http://forums.familytreedna.com/showthread.php?t=41783

The real answer may be buried in the forum. But we did not have the time to wade through the 1,000 or so give and takes. For a recent problem with two files we had, the tool mentioned in the forum (http://www.mapmy23.com/tools/ancestry_ftdna_fix.php) worked for us. Not 100% sure but it appears the issue may be Ancestry switching the RSID base model they use to label their file format. Don’t get us wrong, syntactically the files look identical. But as reported by the tool fix, almost all the RSID’s numbers had to be rewritten. Now are they different RSID’s that are in the same “position”? Is this is a Build37 vs Build38 issue? We know Ancestry, 23andMe and LivingDNA are all using a new array chip that has different SNPs. But it seems something different from that. Something we will watch for and update as we discover more reliable information. Hopefully, it was not simply a server issue at FTDNA that corrected itself with “time”. We did try the old format file in yet another new account and it did still not work though ...