evil if the payment was due out yesterday then depending on who you bank with, there's a fairly high chance it won't come out until Friday due to bank holidays etc. Was it your first rent payment?
As for letting herself in this is utterly fucking stupid on her part. I don't know if you remember my issues with my ex landlord but she could actually be done for trespassing for this. Check your tenancy and English law but you are allowed a few days grace (I think 3 working days) for a payment to be late, and her first port of call should be to write to you or phone you. She shouldn't even come to the house without giving you 24hrs+ notice.
Definitely say something. Keep it light this time, a friendly apology and a promise to get it sorted. But I would also say to her that due to your do history you are very nervous of having people in your house and will not hesitate to phone the police next time. You are perfectly within your rights to do this (my landlady got done for harassment amongst other things for doing just that) Good luck, PM me if you need any more advice.
And merry Christmas all!! I am soooo excited!! and so hungover 