I did my first install of Websphere 6.1 the other day on HP-UX and ran into a very strange problem. Profiles are now managed through the PMT, the profile management tool. After doing the initial install, I started the PMT through the first steps wizard and the PMT launched, but the screen was blank. I didn't see any buttons or anything to click on, which was odd since the websphere install itself worked fine with my X server (I prefer the free XMING, or you can use Cygwin inside of Windows). Due to security restrictions on the VPN I was connected to, I was unable to try the built in X server on my Macbook Pro, so I was stuck inside of Windows.
I did some googling and found this article on an IBM forum:
http://www.ibm.com/developerworks/forums/thread.jspa?messageID=14238812
Apparently this is a known issue and the only X server on Windows that works as of today is Exceed, which of course isn't free. I had to download the trial, install it, and then magically I was able to see the buttons to do a GUI based profile creation. Not cool, and I hope IBM fixes this fairly soon to work with other X servers.
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