It was still there in 0.0.4-4, but after changing the amount of time in the n900 settings when backlight goes off (to 10 sec to finish testing quicker and back to 30 sec) i can't reproduce it. So it works now on my n900 as well.

So nothing's lost ;-) I'd like to give you my detailed idea of an implementation for easier later consideration.

It is giving each dish an option like "overflow mode" or "overflow when counted to zero" or "count across negative values" and then give the start button and the time counter yellow colors.
When reaching zero the stop button continues to be displayed because the timer is still running (now in red color).
When the stop button is tipped the amount of overflow is shown in the time counter bar (no reset to zero) and the yellow start button appears.

little problem: the "abort alarm" function of the time counter bar collides with its "pause counting" function when counting across negative values.

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i've got another feature request:

I'd like to set each item of the config screen if additionally shown in the drop down menu for quicker access. "custom wav alarm" could be moved to the config screen.