Thanks for your help.
The computer in question was a brand new one. I installed 11.0.00 to it directly from my aip, which worked great. I then made a new aip that was patched to 11.0.01 and it gets the error about there being an existing installation. In the short term, I'm not sure if it matters - I may wait to update anything til this latest exploit is patched anyway, but for the long term I'd like to make sure I am doing things right.
Just another little note - I can run the msp file against the computer and it patches the install just fine, just can't run the full install with the transforms.