I think I agree a little bit with what Tracie said. It sounds as if your 3-year-old kind of "gets away with it" since time outs and sending her to her room only last for a few seconds before she's out and causing trouble again. Basically it seems like you're saying that "I try to punish her, but nothing sticks, nothing really works"
Your 7-year-old, on the other hand, sticks with the punishment you give him, but it's not really changing the behavior for him, either.
I have a 3 year old and time outs *do* work for him. They didn't at first (we started using time out when he was right about 2, I think), but persistence of us telling him "NO, you do not get up when we've put you in time out" or "no, you cannot have a toy, you're in time out" finally got the point across. And now when we put him in time out, he knows he has to sit there and wait for us to come and talk to him. So, maybe you can work a little more with enforcing the time outs or staying in her room with your daughter? I know it's not easy, but it might pay off in the long run.
Otherwise, "punishments" only really work when it's something the kids care about. You said that taking away tv and toys doens't work because the kids don't care. If you can't think of anything that the kids really really care about and will miss if you take it away (say desert after dinner or a special activity they look forward to doing on the weekends when you're not working?)... change tactics. Maybe reward the really good behaviors instead? Tell them that if they can get through you fixing/everyone eating dinner without a fight they can have X (whatever they might really enjoy and *want* bad enough to be good for). Then legnthen the time they have to be nice to each other... say 3 days, then a week, then 10 days before the next big reward. Use a sticker chart and everything - it'll help you (and them) keep track of their progress.
It's just an idea and I know a lot of parents don't like "bribery" but I find that with my 3-year-old, it works. And as long as I keep *most* of the rewards being praises and hugs from me (on the days he's nice to his brother I tell him all the time what he's doing right, praise him for doing well, etc. and every now and then if he's gone a long stretch without me having to get onto him - and for him a long stretch is 3-4 days, he's still only 3 - then I'll say "you know what, you've been really good with your little brother lately, would you like a new matchbox car or a new thing of playdough?"). The material rewards aren't set in stone and are random, so it's not like every time he's nice to his brother he's demanding a treat, but it does help reinforce the good behavior.
Doing positive reinforcement along with the strictly enforced time outs when he's not having a good day have really helped his behavior immensely, so maybe something like this could work for you.
Good luck.