Sorry, I just re-read your post and realised that I've managed to get my wires crossed - the issue you're experiencing is not that NCrunch isn't auto-enabling, it's that you always get the wizard ...
The wizard has nothing to do with the auto-enable feature. It's controlled very differently.
There are two mechanisms underlying this feature, storing state in two different places. One is inside the .ncrunchsolution file, in the form of the 'FileVersion' property. Where the FileVersion does not match a value of '1', NCrunch will run the wizard with questions specific to the solution itself.
The second mechanism is in your global configuration file, under your user profile.. i.e.: C:\Users\Remco\AppData\Roaming\NCrunch\globalconfig.crunch.xml .. This also contains a FileVersion, which on the latest version of NCrunch will need to have a value of '2'. If this isn't the case, the wizard will be run with questions specific to your global configuration (i.e. CPU config etc).
Note that after NCrunch has saved configuration to both of the above two files, it will update the FileVersion properties accordingly and you shouldn't see the wizard again.
Considering that you've already checked over the .ncrunchsolution file thoroughly, I wonder if it's the global config file giving you trouble. If NCrunch isn't able to write to this file, you'll probably see this issue. You may also see this issue if you're running two very different versions of NCrunch in different versions of Visual Studio. For example, if you are running NCrunch v1.48 on VS2010 and NCrunch v2.11 on VS2013. The config file is shared between versions of NCrunch in a way that would probably cause these two versions to fight over the FileVersion property.