Sorry, disable package configurations? If I did this the package won't pick up any configurations I put in the configurations tab of the SQL Agent Job will it? Or do you mean, do as I did earlier in this post and leave "Enable package configurations" ticked in BIDS for the package but remove any configuration files in the package configuration window, putting whichever configuration file I want in to relevant SQL Agent Job's configuration window? Or are you referring to the Set Values tab in the SQL Agent Job? If the last one, I have around 80 of these variables so will be difficult to maintain.

Is there an alternative to what I've done here then out of interest? If so, I'll try and apply that with my next SSIS package. Probably gone too far with these for now if removing the package's attached configuration file will work.