Javascript confirm() popup freezes everytime

Since the latest update to Firefox (3.6.4), 3 of our users have reported that Firefox crashes when calling a confirm() dialog. The dialog appears but no buttons work and the dialog cannot be moved or closed, and the process seems to have hung.
We have tried Safe Mode and the problem persists.
The HTML page in question, with the confirm() call, is a local file with one embedded Flash applet.
After about 30 seconds of waiting and clicking around, the process suddenly recovers and acts normally from then on.
Anyone else having this problem?

additionally, i want to add that the problem does not occur on all confirm() calls, for instance this one works fine:
http://www.tizag.com/javascriptT/javascriptconfirm.php

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