EB Cobalt flats have been the only flatwounds that I can tolerate the tone of. I usually use roundwounds but have EB Cobalt flats on a couple of basses. I haven't really had an issue with unbalanced tension, but I wish they would make an even lighter gauge than their 40 - 95 set. Also, I've had intonation issues on SOME of the sets I've installed on the G string. It's really weird in that I have to crank the saddle back as far as it will go sometimes to get the intonation on that particular string right (the G string). On one bass I actually had to remove the spring to get the saddle back far enough. Really weird. It doesn't always happen, just on some sets I get. I haven't really been able to figure out why some sets have that issue and some do not. Nothing really looks any different.
As for light gauge strings: I have a theory as to why I do not like flatwounds in general, and it goes beyond just the flubby slow-attack sound. The lowest tension I've used is TI flats. I really don't like the sound of those much. But, my theory is that half the reason I don't like flats is just the typical high tension. I just installed a set of really, really light gauge Dogal "Jaco" flatwounds on a bass and so far it's been very interesting. I might open a thread about that. They are a bit brighter than typical flats in a different kind of way than EB Cobalts are. Especially the D and G string. But the tension bendability is way, way more to my liking. It's the ONLY set of flatwounds I've ever played (and I've played most all of them at one time or another) that thumb-and-slap snapping the D and G string sounds REALLY good... pretty much just like a roundwound. I think that has to do with the super light gauging. This gives me hope that I've found another set of flats that I actually like the sound of AND feels good under my light-gauge-loving fingers. Too bad Dogals are crazy expensive.