You should also read the section on "considerations":
https://products.butterflylabs.com/homepage-subproducts/65nm-asic-bitcoin-mining-chip.html
The upgrade is from 5GHz->7GHz, that's 40% faster hash. BFL states overclocks are possible only on high-grade ASICs from 250->294 MHz. That's only a 17% overclock...no enough to get you 40% higher hashrate.
So the upgrade likely involves cherry-picking the better ASICs. Getting one of the 60% of chips have all their engines working, and out of those, one that will also stably overclock to the higher frequency.
I'd say if >40% of the backlogged customers go for the upgrade, they could have issues keeping the order of the queue without injecting further shipping delays.
Well, my prediction on this issue turned out to be the eventual outcome.
Read'em and weep:
https://forums.butterflylabs.com/blogs/bfl_jody/251-monday-july-22-2013-shipping-update.html
This is the classic risk behind offering a cherry-picked component for profit, and ending up with a huge share of customers ordering the tail of your distribution.
If the imbalance in share of upgraded orders vs. availability of faster ASICs persists through the queue (no reason to think otherwise), the difference in ship dates for regulars vs. upgrades units will increase non-linearly.
Silver-lining: if your Jala order date is beyond Dec'12, cancelling the upgrade and trying your luck overclocking yourself will surely help get your unit earlier.
Confirmed by BFL_Josh
https://forums.butterflylabs.com/pre-sales-questions/4031-2gh-upgrade.html#post49429