Internet Explorer for certain user profiles cannot be reset to properly show certain pages.

We have Windows 10 Enterprise on various versions 1703, 1709 and 1803.  We have an external website we use which was recently updated by a third party.  When we log into the site, some features do not work as the code appears to be newer and IE defaults to document type 7 on mostof our machines.  If we log in and switch the emulation to IE 11 once logged in, it works fine but this is only a temporary fix.   Some of our machines work fine and others don't.  We have ruled out Windows updates based on the fact that machine with exact same updates, some work some don't. We have cleared caches from within IE and reset IE from within IE with no luck of the application working.  We have also removed "HKCU\Software\Microsoft\Internet Explorer" in an attempt to reset IE but it doesn't appear to fully reset.  On further testing, we have found that if we create another user profile on the same machine, it works fine so this may be related to the user profile.  Another thing noticed is it may be related to using Microsoft tools to pull and plant profiles on computer rebuild but we have not made this determination 100% but new builds without copying profile seem to be the ones working fine.  Are there any other suggestions to try or any other way to fully reset IE for a specific user profile?  Unfortunately, we have hundred of machine and while we need a solution, we would also like to be able to automate it as creating new profiles on every machine would mean complete reconfiguration of a number of other software we have on the machines.

Thanks
Brad