Showergelfresh, I'm quite sympathetic with you. I know I don't like it if i babysit my gc and then my dd complains about some little thing or other. It must be hard to face that once or twice a week and not even know when dil might be around. Hugs!
I'm glad the comments here have given you confidence to speak up and ask about things ahead of time. Also, I'm glad dil's attitude seems to be better for whatever reason.
I have to agree with those who say that "working till 5" is 'working till 5" no matter where one is. And if dil is communicating with colleagues on the Internet or meeting work deadlines, she may have to remain within that time frame. Same if she wants to be done by 5 so she can spend a nice evening with ds (her dh) and gs later on. Therefore, I can see where she can't really stop to go collect gs, anymore than if she were working in an office.
Truly, you are doing her a huge favor. And if it were me, I would be ok with just about everything, as long as I knew my child was safe and happy. She still probably wants her child cared for the way she would do though. So if she cuts his sandwiches up, then why not do that? As for the pens, I agree with the poster who said to let her know you usually clean up at the end and ask if she prefers if you do it as you go along - that is, if she raises that issue again.
It does seem clear that you tend to do some things she doesn't want or you wouldn't do the peanut butter differently when she's there. Imo, if you know she only wants him to have a thin layer of pb on his sandwiches, then you need to adhere to that. Most likely, she thinks it's healthier, and she has a right to make that decision for her child. Contrary to what some posters have said, a hired nanny would be expected to honor the mum's wishes, period. Of course, unlike a hired nanny, you're not getting paid (not in dollars and cents, anyhow). But would it be so hard to do things her way? If gs wonders about it, you can just say, "Mummy says this is better" of something like that.
If you balance your newfound confidence with a show of more respect for her, I think things will just keep getting better. You sound like a delightful gm, and I hope you continue to enjoy your time with gs and whatever time you get to spend with the other one, also.