Tim.
Hi. We are also getting a few reports from our students saying that they are getting a score of 0 when they submit a quiz attempt despite having answered the questions correctly. We are using your "favourite" feature - the secure window! 
I haven't been able to reproduce the problem though - it's random... But we are trying to get more info.
In one case the quiz has a time limit of 45 minutes. When I review the students attempt it shows that the attempt took 48 minutes and the score was 0. I regraded the quiz and the students answers were recorded - I could see their answers. But their result was still 0, despite some of the answers being correct. The quiz is set to auto-submit when the 45 minutes is up so I don't know how the attempt could have taken 48 minutes. Normally, the counter displays correctly and 'flashes' the different tones of red as the clock reaches 0. When it reaches 0 the attempt is submitted and the secure window closes by itself. The only time it hasn't worked was in this one instance - we had more than 450 students submitting one quiz yesterday and only this one complaint.
I will post more info if I manage to reproduce the problem or to find the cause.
Our setup:
Moodle 1.9.4+ (Build: 20090204)
Windosw Server 2003 SP1
IIS 6 & FastCGI
MSSQL 2005
FreeTDS (build supplied by Eloy)
PHP 5.2.8 NTS