My guess is that this is being caused by a member/officer of your guild that might be in another guild (perhaps an alt on another server), and that character's profile and bank information is also being uploaded, effectively wiping out the information.
The easiest solution is to change which rank has control over "member" in Feature Access. Or ask which members of your guild who have "member" access are running the DKPProfiler.
as of the time this ticket was opened, I was the only one running the addon. Also since the infomration is character specific and the DKPSystem handles multiple guild, it should handle the senario you describe. Also, wouldnt the senario you describe not emty the guild bank but make it the wrong stuff?