This is not erroneous behaviour: it's perfectly normal.
Here's something I've proposed on Area 51. Look at the right: It shows that I have 6,778 rep at the time of this writing.
Now let's look at my network flair:
At the time of this writing, it shows roughly 5,300 rep for my network-wide account.
So Why the Difference?
Area 51 includes the site rep for all sites that you have earned 200 rep on, whether your account is funky on one site, or another site is deleted altogether. Let's break my rep down:
- Open Source: 2647 rep
- Stack Overflow: 1829 rep
- Aviation: 536 rep
- Area 51: 289 rep
That's about 5300. I've earned rep on deleted sites as well, and then I have rep for this site too.
Why is it different?
Area 51 rep is supposed to be an indicator of the effort that you put into other sites. So it would be kind of unfair to just say that you didn't put effort into a site that was deleted for other reasons, or for anywhere that you are suspended. Area 51 takes all the rep that you have earned, whether you like it or not, to make your Area 51 specific flair. I have 6800 rep on Area 51 because of my contributions to failed betas, not because I'm special.