Hi, Dapper.
I am going to break your post up and deal with each thing. Apologies if I say something you already know.
So ive been having massive problems with compiling maps as they are taking 2+ hours to get out of the vbsp stage
It may not actually be VBSP that's causing the compile to take a long time. VBSP shouldn't take more than a few seconds, really. VVIS can take a while since it needs to calculate the visibility between every 'portal' in your map (a side of a visleaf). if you have a map that's quite large and open, then much of it may be visible to itself so it would take a long time to calculate. It's why mappers build their maps consisting of great walled-off sections, typically using skybox brushes. If you feel this applies to you, hunt down a guide on visibility optimisation. There are a few.
If you compile in Hammer, the compile log will seem to freeze, because Windows thinks it has hung. If you use a third-party compliation application such as
CompilePal, you will be able to read the log in real-time.
and looking at the files that do compile versus the ones that dont reveals that the files that dont are saved in .rmf format and whats more i cant save in vmf format anymore, its not on the drop down menu when saving and coming through the options menu reveals nothing. has anyone had this problem and or am i being stupid and there is an easy solution
I've never heard of this problem. If you manage to eliminate those dodgy compiles you will probably sort out this issue, but your original VMF shouldn't be affected like that. If you like, upload your VMF somewhere and give us a link, and we will take a look and point out problems.