Oh man, this is a good one. This is the problem that never seems to go away. Everybody has the best way of doing something. Apparently, we Americans are worse at it then the Europeans according to a survey I read maybe 20 years (still true?). The Europeans were/are more amenable (and smart IMO) in adjusting their internal processes to adapt to new software instead of the other way around which is how it's usually done here in the U.S.  You would think that management would want to take advantage of the opportunity to improve a process and the wholesale opportunity this can provide. Instead, it usually follows the path of least resistance (which is to not disrupt the status quo) and you can end up with an even worse process that's been 'Frankensteined' to an older one that nobody is happy with in the end, tens of millions of dollars have gone down the drain (the vendor and consultants win of course), careers are over, tears shed, friends lost and plenty of emotional scars for anyone involved in the project. Dramatic? Its' an understatement of the reality.
I can see militantly preserving your propriety business process that makes you money but your HR process? Procurement? Help Desk? etc. etc. I suppose it comes down to a lack of will or ignorance on management's part to push through an implementation plan when it meets resistance and the IT people for not doing adequate process analysis and planning or just not adequately educating management about the opportunity.