It is true you do have to be VERY rigorous about touching in and out of EVERY station or speaking to staff at the time to get them to resolve things. As an example when I went in through London Bridge about 9pm last night the barriers weren't working and wouldn't let me touch in, staff said there was nothing they could do and I should just get on the train. I was quite prepared to resolve this at Forest Hill but as it turned out the gates were open anyway.
I don't think there is any limit over which pay as you go relates to monthly travel cards although I think there is a daily limit of not more than the equivalent off peak one day travel card, plus any peak travel costs (or a peak travel card?).