This is a bit old, from May, but anyhow...
The patch to implement anonymous pipes on top of named pipes: http://www.winehq.com/hypermail/wine-cvs/2003/05/0305.html along with a corresponding bug fix: http://www.winehq.com/hypermail/wine-cvs/2003/06/0123.html causes Xilinx ISE to run really, really slow.
It has a window to which messages are sent via a pipe, and what I see now is that one line comes out every 2/3 of a second or so, as regular as a clock at least by eye. I can revert those two patches, and it goes back to spitting out the messages very fast. Since there are a lot of messages being sent, the current version slows the app down to a crawl.
It does not look like the patch itself is the problem; I am guessing that it is the underlying named pipe implementation that is the problem, which was exposed by the patch.
Also, reverting to the full CVS 5/20, just after the pipe patches, has the same problem. So it appears that whatever is wrong with named pipes (if that really is the problem) was already there on 5/20, rather than it being something introduced since then.
Any hints on what I could look for would be welcome.