There's an error when you set the quota for the first time.
What SABnzbd should do is set the "quota left" amount to quota minus the downloaded amount in the current period.
(So, the available quota reduced with what you already downloaded today, this week or this month).
Instead SABnzbd sets "quota left" to the already downloaded amount, which is clearly incorrect.
The problem will go away once the end of the first period is reached.
Unfortunately I only discovered this a day after 0.7.1 went live.
So, the next release will contain a solution.
I cannot reproduce the behaviour where deleting items will change the "quota left" amount.
You also don't make clear whether you're deleting "old" items in the queue or in history.