When I resume from hibernation in FC5 I loose the hability to select the operating system to boot. i.e. when I first installed the system, I could hibernate linux, restart the computer and boot into windows. After updating the kernel, grub boots linux inmediatly without allowing me the choice between both operating systems. I have been trying to find what boot options I need to modify (if any) in grub.conf but I haven't been able to. Any ideas?

I am not sure about this but I do not think it is safe to boot into one OS, hibernate, and then boot into a different OS. Without doing an actual shutdown you could get some type of file corruption. I think a log file dealing with the information stored on a hard drive does not get written without a shut down so when you go into the other system some changes to the hard drive for the other system may be lost or some other bad stuff.
I have been told to always shut down properly before booting into a different OS. SO if there is a power failure or something I always boot into the system I was previosly in and do a proper restart.

Well I used to do it all the time and never had any problem. Windows and linux are in completely different partitions, and I don't mount the windows ntfs while working on linux, and windows does not have access to the linux ext3 partitions, so I don't see how there could be any file corruption issues.