I'd say it's an issue with the stock 2.2 code. It's a bug that should have been quashed, but probably got overlooked. Glitches like that are annoyances, little more, as long as you're working with a known strong signal -- unless you start dropping connections. My phone usually shows higher signal strength than it should, unless I'm using the WiFi scanner program I downloaded from the Market. Of course, I almost never have access to a WiFi network to connect to.
I don't think the root access has anything to do with it. The thing to do would be to see if it happens across a sampling of 2.2-based ROMs compared to a sampling of 2.1-based ROMs. However, that might take days.Since this is a short-term project, I'd say your best bet would be to get a baseline for the problem with a stock-root ROM (you have) and then compare it to at least four source-built ROMs of varying custom code levels. If the problem is endemic than it could be a hardware incompatibility with the "improved" WiFi code in 2.2. If it's not then you know it's the stock code causing the problem.
I think you're right about it being a problem with the code, since the signal reports accurately in the settings, just not in the bar... though I didn't even notice it was an issue in 2.1 until xmguy pointed out exactly what it was doing. However, this definitely has not been a short term project. I've been testing this since the first Froyo leak. So that includes the "stock" leaks from p3, Sapphire .8.4 and 1.0 (source), Simply Stunning 4.5(maybe 4?) and above (again, source), UD 5,6,7, metiCkOne, Kangerade. I need to try CM and see what happens there.
I don't think it's endemic, but who's to say for sure unless I grab a Droid that doesn't do this and see if it holds the wifi signal any better than mine, which is typically decent anyway. Since I mainly use wifi at home, it's (like you said) a small bother more than anything else, as I know my wifi signal. But if I traveled a lot, it would be annoying, b/c the signal reporting would be unreliable. However, xmguy, and now Metalunna, are the only ones I've ever come across that have the same issue... so it's very weird, but not widespread.
edit: lol... well I've gone and flashed 2.0.1 and evidently Verizon's activation system is down for overnight updates or whatever they do late at night... I should know better! So now I'm definitely done until tomorrow.
