UPDATE: I finally got through to the IRS!
I have had a mixture of helpful and unhelpful agents. The first agent was extremely helpful, and she said that if I have a different result to what the IRS has, and the IRS changed/adjusted my return, they should have sent me a notification (CP11 letter). I have not received anything. As I have a different result for line 28 (1040) as they have, I would either submit an amendment or re-submit, however she wasn't sure which (amendment would be much longer). She said Tax Law (division of IRS) should be able to help me, so she transferred me to them. I got straight through, however the lady on the phone painstakingly went through all my numbers asking me to give them to her to see if I was eligible for the ACTC. I had done all of these and I know I am, and she got confused throughout, but then came to the conclusion that I was eligible and my calculations were correct. When I tried to get her to give me the advice the original Agent said Tax Law could give, she couldn't and said I should be transferred back to the main IRS to see if they did have on record sending me a CP11 letter.
After all this, I got through to an extremely helpful gentleman, who said he could see what the problem was. The IRS had amended line 28 to "0" on my 1040 but I had still claimed $2800 on my refund lines. He went into form 8812 and could see it was "damaged" hence he believes this is why they changed it to 0 because there was no evidence for the $2800 claim (intact form 8812). He said the IRS should have sent a letter if it was damaged like that so from his perspective this was not correct procedure.
As it was end of year and systems were down for update, he said I should ring back from Mon 3rd Jan and get an agent to update my 1040 and 8812 with me faxing the forms to them. He said they should be able to do it then and I shouldn't take no for an answer, because they each have a personal fax number.
Now I am on the phone waiting for a free agent, with an online fax service at the ready. Finger's crossed....
Thanks for all the responses, and happy new year all.