Here are published quotes from both sides.
“We regret we had to make the decision to stop accepting FTDNA [FamilyTreeDNA.com] DNA uploads. FTDNA has threatened to sue GEDmatch over claimed privacy issues. We have been asked not to discuss the details, because it would be to FTDNA’s disadvantage. Suffice it to say that FTDNA’s own site seems to currently violate these same issues.
“We would prefer to work closely with FTDNA in solving this problem to everybody’s benefit, but we have not received a response to any of our suggested compromise solutions. The technical obstacles to satisfying FTDNA current demands are significant. It appears that our only alternative may be to remove all FTDNA DNA match results from GEDmatch. The issues raised by FTDNA do not apply to kits from other testing companies.”
The Family Tree DNA (FTDNA) website states:
“We have reached out to GEDMatch expressing our concern that their website could potentially lead to a breach in privacy of our customers. Given this, we proposed to discuss the subject with them, but in parallel we suggested that until further clarification and assurances that the privacy of our customers’ records are protected, Family Tree DNA uploads should be suspended. We hope that with the cooperation of GEDMatch we can reestablish the uploads in the near future.”