Sounds like you are doing too much fiddling beforehand. Just follow the profiles install instructions.
I have strongly objected to profiles putting modules in a strange place as then when you install some other (non-profile contrib module it winds up in the normal place and using the web based update a module puts it in the normal place with the result of having two copies of the module and not knowing for sure which one is actually used - bad deal). So you really have to rely on the distribution provider to keep up with security patches to modules they use.