I think she's just being mean. I have so many friends who complain about having similar experiences with their MIL. I think they know they're being annoying, and they do it with gusto. My own MIL never picked on me about my kids' sizes (which is really surprising because all of their cousins are huge yet my kids are really skinny) but she'd always have something to say about their clothes, and what type of toys and "activities" I was or wasn't exposing them to. My kids were big time droolers when their teeth were coming in. Sometimes their shirts would be soaked through as though they spilled a cup of water on themselves, so I made them wear bibs all the time to keep their clothes dry. She'd always tear the bibs off and say that it was tacky to leave them in them all day.
Or she'd even say "Your kids are not being stimulated enough. Don't you ever buy them toys?" We had tons of stuff. But I'm a neat-nick, so unlike my SIL's, I kept all of my kids stuff in toy boxes, on shelves or in their closets. She knew we had tons of stuff. Heck she bought alot of it. But she'd still try to be nasty.
I'm certain if I left toys all over the house, and my kids were big bruisers she'd have something to say about that too!
I say, don't worry about her and her comments. It's probably just a power-trip on her part. She knows it bugs you, so she'll continue happily until it's not fun anymore, or she finds something else to get your goat. :(