Okay so here was my situation:
I have two PC's; one had not been finished and had a blank HDD in it. The other had Vista Ultimate 32-Bit on it. The unfinished PC is going to be a secondary PC that I can use whilst at home and will have the HDD from the other PC with Vista 32 on it.
Still with me?
The other computer is a high performance PC i built which I use whilst at Uni and will have Windows 7 Home Premium 64 installed.
Whilst installing Windows 7, I left both the blank and the HDD with Vista on it inside the PC. I installed Windows 7 with no hiccups on blank HDD. Everything works fine - I can access the other HDD with no problems etc.
So here's when it goes wrong: obviously, I need to remove the Vista HDD to put in my other PC. But when I do that, it says 'Boot MGR is missing, press ctrl+alt+delete' etc. When I put the HDD back in, suddenly it works fine.
It may be worth saying that with both HDD's in I can select which OS to boot into - which I believe is how it should be. I have tried using the OS repair disc to no avail - no problems are detected...
Apologies for making this post rather wordy but I thought it best to explain my situation as best I could. I am also aware that another member has experienced similar problems, however his circumstances appear different enough for the need of another post.
Thanks to all those who can help!