OK, so we ran into this problem, too.
Upgrading to 11.20 SR5beta is not an option (no early adoption of "latest and greatest but still buggy service releases"), but we need a solution for this problem.
In some little tests we found out that the plugin itself (11.20 SR3 and 11.20SR4) seems to work perfectly (manually written adresses or links) but your server will recognize your IE11 client as "unknown" and therefor not presenting the IE-Plugin-Links in Accesspoint.
We also found out that the recognition of the client must be in
C:\Program Files\QlikView\Web\js\accessPoint.js
on our server.
If someone would be able to add "real" IE11 entries to this file (there's already something commented out...), this should fix the problem...
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