My site is Gleeson.us (http://www.gleeson.us/). There are two sites which I designed, SleepyKats (http://www.sleepykats.com/) and Adventures In The Wild (http://www.adventuresinthewild.us/). Gleeson.us links to those two (because they are examples of my work), and they backlink to Gleeson.us (as a design credit). All three sites have had a PageRank of 4 (for their home pages, that is) for many months.

Now here's what's weird. Do a search for link:www.gleeson.us on Google (http://www.google.com/search?q=link%3Awww.gleeson.us), and the SleepyKats page is included, but the Adventures page is not!

Link farm penalty? Could Google be interpreting these backlinks as a "link farm," and not counting them as natural links? But then, if that is so, why include SleepyKats but not Adventures? It must be something that is different between those two sites.
Invisible text penalty? My best theory is that Google sees my backlink on Adventures as "invisible text." Of course it isn't invisible, I would instead call it tasteful. (It's light gray on a white page.) But that's the only theory I can think of to explain why it treats Adventures differently from SleepyKats.

Does anyone who knows more than I do have a better theory? And does anyone know exactly how much contrast is needed to make text "visible" to Google?

Sometimes Google doesn't show all the backlinks it actually recognizes. Therefore the "link:" command is not to be relied upon.

This is most likely what is happening in your case. I very highly doubt it is either of the two reasons you state because neither of them exists. You are not a link farm and like you said, the link from the second site is not invisible.

Sometimes Google doesn't show all the backlinks it actually recognizes. Therefore the "link:" command is not to be relied upon.

This is most likely what is happening in your case. I very highly doubt it is either of the two reasons you state because neither of them exists. You are not a link farm and like you said, the link from the second site is not invisible.
I agree... there seems to be a little arbitrary nature in the backlinks... no hard and fast rule applies...

I have had PR6 links show up and disappear. it is totally random what that tool shows.