Version: 4.1.00 (KDE 4.1.0) (using 4.1.00 (KDE 4.1.0), Debian packages)
OS: Linux (i686) release 2.6.26-1-686
This is a regression and has been fixed in 3.4, already (see #78354).
As #123504 is pointing out, the cookie dialog should be modal and block the UI of the requesting Konqueror completely. This is the only sure fix. Note that it should not block other instances of Konqueror.
I am setting priority to high and severity to grave as this bug can block surfing completely and in a (at the time) non-obvious fashion.
Setting back priority and severity to acceptable values.
Have a look at http://bugs.kde.org/bug_status.html#severity
*** This bug has been marked as a duplicate of bug 160044 ***