Hi Tomasz,
I got same problem in Windows Server 2008 R2, however its working on windows 7, we can install webadaptor 2 times using same installer. WebAdaptor is web application act like reverse proxy, so the workaround for this issue is duplicate your existing webadaptor as second webadaptor.
here is the detail steps: (i assumed you used IIS and installed webadaptor on inepub/wwwroot/)
1. wa already installed, and you name it 'waportal' > don't register anything in here (portal or arcgis server)
2. go to c:/inetpub/wwwroot -> copy 'waportal' and paste on the same place c:/inetpub/wwroot/
by default second wa name is 'waportal copy'. rename it, for example 'waserver'
3. you have to convert 'waserver' as application. go to IIS Manager > in the left side expand Default Website > right click in waserver, choose convert to application
5. you have 2 wa right now. the first is waportal and the second is waserver.
a. register your portal on your waportal
go to http://yourhost/waportal/webadaptor/ > select portal for arcgis then follow the instruction
b. register your arcgis server on your waserver
go to http://yourhost/waserver/webadaptor/ > select arcgis for server then follow the instruction.
it's work for me,
Amri