I've only read Carnival, which had similar --and other -- problems for me (...for a novel set on a frikkin' martriarchal world, it is depressingly full of Fail when it comes to the Dykes to Watch Out For test, and don't get me started on the boy genius).
I don't know if you go for Doylist explanations, but I gather that Bear has issues with her lesbian mothers which may affect her writing of lesbian characters.
Carnival was one of those novels whose enjoyment for me was considerably lessened in retrospect. At first I had problems with how much of the plot seemed left to hang in mid-air; then I started thinking about the premise of the universe and realized I didn't believe in it; and then I realized how much the characters seemed focused on "the goodness of the male," rather than on how the society might be genuinely different with women in control and offer something to women that male-dominated societies didn't. (Many of the women seemed relatively unhappy, because- of course- they wanted relationships with males that the society disapproved of).
Huh. I didn't know that. I generally try to stay away from biographical explanations unless the author freely admits it (like Steven Brust admitting the divorce his character goes through is reflective of his own divorce). What disappointed me about this was that Bear does seem to make a conscious effort to deal with issues of race, sexuality, etc., and so I'm very surprised this blind spot exists.
The problems with Carnival started fast for me, and the ecological world-building which could have been interesting rather made the political world-building worse.
This LJ entry may be TMI for you (I skimmed it), since it's a big, autobiographical confession of personal trauma, but it refers to the source of some of those issues:
Salient quote, referring to the woman with whom she & her bio mother lived: "She was also a really nasty-ass lesbian separatist, but I try not to hold people's crazy politics against them. And besides, I got a book out of it." (Although Bear doesn't specify which book, & I don't want to wade through too many of her personal entries to look for more information.) She makes references to being raised by lesbian separatists elsewhere, in discussions of feminism and so forth, which are less loaded.
With the ecology part, I was left wondering uneasily how much of the attitudes involved were a target for satire, and how much Bear really meant (does she think all environmentalists are that extreme?)
*skims post* Yeah, I can see now where the issues might come from. Although it's notable that Carnival is not really lesbian separatist, I do have to wonder how many of the issues with lesbian separatism translated into the depiction of a society where many of the women seem desperately unhappy and even afraid of ruling over men.
This made me wonder why Carnival didn't bother me *more* - I think I read the argument as "socially constructed roles based on genetic features suck," not "patriarchy sucks." Thus, it didn't bother me that women were unhappy in a society with strict gender roles - even if theirs happened to be powerful (and any group could be justifiably worried about the ethics and sustainability of oppressing half the population - I didn't read "afraid of ruling over men" as a negative, Pretoria's situation in particular seemed like "I would like to support them, but don't really know how, from my privileged position, to do that" - maybe that's because condemning feminist guys in the real world as "afraid of ruling over women" really, really disturbs me). Vincent and Michelangelo are operating outside of their strict roles, so they come off as more free/better in the window of the novel - but viewing sexual orientation as an innate trait, their socially constructed role based on that is outcast, which didn't work either.
And the very-not-human alien species does have social roles based on genetics, which works for them, precisely because they aren't human.
Incidentally, somewhere in her blog, she mentions that Carol and Autumn (lesbian couple from Whiskey and Water) have the most healthy relationship she's ever written. Wish I had a citation, but I stumbled on that a long time ago.
Sorry for the length of this, I've been on a Bear kick lately, and the thread was fun to think about.