  My First Guess Duf, as a woman with (fairly) normal womanly traits, I know how we have tendencies to express something (perhaps very strongly), while actually being concerned about something totally different. Here's what I think is happening: Mrs. Duf is frustrated. She's under a lot of pressure and as a modern woman, has taken on many roles: 1) Super Mom, 2) Career Woman, 3) Wifey of Duf Fer.
Personally, I think there is more pressure on the woman to be perfect at all Three. Men can slack a bit on #1 or #3 and get away with it because "they're bringing home the bacon". Of course, this is crap, but society (or the horrid media) dictates this. (Another reason I still wish it were the 50s. ) So when Mrs. D says "things need to change around here"...you may think she's talking about the order of the house. (Men tend to take things more literally than women. ) However, I think she just wants you to be aware that she's going to need your support. Not just with the vacuuming or putting Tiny E to bed, but emotionally as well. She needs to know you'll be around to pick up the slack.
Also, you traveling a lot probably makes the Mrs worried about things falling behind at home. Talk to her and tell her what you told us in your post. I'm sure she's more concerned with the cleanliness of your relationship than with the bathroom. Convince her that you have her back... But again, this is just my guess. 
