Are you using the Canon brand ACK-E6 adapter or is this a 3rd party adapter?
I own a 5D II and while I do own the adapter, I haven't tested that particular arrangement. I _DO_ use the ACK-E6 with my Canon 60Da (astrophotography camera) all the time ... while the USB is connected to a computer which is remotely controlling the image acquistion at the telescope and I have never had an issue.
My 60Da is still in-transit (along with the ACK-E6). I was at an astronomy event last week. When I get it back, I'll hook up the ACK-E6 to the 5D II and see if I have the issue you describe.