Sorry jbignert, usually I'm not one to pile on, but I'm going to have to nail you on this one also. If your support crew doesn't "know" about this issue it is because they are incompetent.
1.) Look around your own forums. There are several threads talking about this.
2.) The information you asked for was requested and supplied at least twice during the farce of an email exchange that was called "technical support." Here it is again:
Evernote Windows client 184.108.40.20627
Windows 7 Pro, fully updated (all updates rated "important" and above)
IE9, fully updated as above.
As for the work-around mentioned by the OP, it does not work reliably, so this is a stopgap measure at best.
The Microsoft issue mentioned in the link you provided is just FUD, sorry to say. That reference is over 8 months old. This issue started with the release of 4.6.1 whereas everything was working fine in December with 4.5.x. Perhaps that issue is related, but it isn't a MIcrosoft problem. The changes your programmers made in 4.6 created the problem.
Looking more carefully now at the OP's problem description, my problem is slightly different, and far more ubiquitous. I suspect that the other posters here have my problem, judging by their comments.
The OP mentions problems only on secure pages (https://) I have the problem on ANY page I try to clip. I never see the "Internet Explorer tried to restrict" message. All I get is a little black box in the middle of the screen which says "clipping" (this is new in 4.6) which often takes far longer than it used to in 4.5.x. When the clip is complete, the only thing placed in the note is the URL placed in the body of the note (and also in the URL field).
This needs to be a high-priority fix. I am certainly skeptical of moving the rest of my organization to a paid Evernote platform with service like this.