One of our clients migrated from Clinicare a UNIX/AIX character based EMR system to a graphical Windows based EMR.  User issues included "what is a mouse", why do I have to set my default printer, I can't find the booking.  I can't stress enough that 1 or 2 day training from the EMR vendor is not enough!  The clinic should have in-house Windows training for sure, but the EMR vendor must recognize the client they converted came from a character based environment.
Other pitfalls un-related to user experience is data conversion.  Ask your new EMR vendor if they have ever converted another clinics EMR data, if not you will be a guinea pig for them and others will benefit from you.  In this case, get a good reduction in the price since you are going to be their R&D!  If the application is being hosted off-site as in a ASP model then make sure the method of delivering the application is fast, reliable and expandable.  Problems we have seen is Citrix, VPN, no accelerators and the EMR vendor taking on too many new clients without address the network or their servers.
Once everything is ironed out and users have figured out the new EMR application things will be smoother but don't forget a character based EMR system will always be faster then a Windows based one!