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Calibre is one of those programs that if you use the official distro version the program will be sorely out of date and won't get any of the recent fixes and updates.
I always use the script and never had a problem. In fact, I notice that there's even an unistall options now:
animedude01@suzumaya:/opt/calibre$ ll /usr/bin/calibre*
lrwxrwxrwx 1 root root 20 2010-03-14 16:47 /usr/bin/calibre -> /opt/calibre/calibre
lrwxrwxrwx 1 root root 30 2010-03-14 16:47 /usr/bin/calibre-customize -> /opt/calibre/calibre-customize
lrwxrwxrwx 1 root root 22 2010-03-14 16:47 /usr/bin/calibredb -> /opt/calibre/calibredb
lrwxrwxrwx 1 root root 26 2010-03-14 16:47 /usr/bin/calibre-debug -> /opt/calibre/calibre-debug
lrwxrwxrwx 1 root root 29 2010-03-14 16:47 /usr/bin/calibre-parallel -> /opt/calibre/calibre-parallel
lrwxrwxrwx 1 root root 27 2010-03-14 16:47 /usr/bin/calibre-server -> /opt/calibre/calibre-server
lrwxrwxrwx 1 root root 25 2010-03-14 16:47 /usr/bin/calibre-smtp -> /opt/calibre/calibre-smtp
-rwxr--r-- 1 root root 2456 2010-03-14 16:47 /usr/bin/calibre-uninstall
animedude01@suzumaya:/opt/calibre$
I'd highly recommend using the script and going with the most recent version. I think it will be a lot less hassle than trying to get it to run under Wine.
My $0.02.
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