yes, the flags in ctf are built into the mod and work differently then the crypt.  the crypt they have to be made from a few different entities where as the tomb only has a single one. 

Dr_Bones, if you can provide us the .vmf it would make things a lot easier to convert it because there are always errors when you try and decompile a map.  usually unless the original mapper is gone, decompiling should be a last resort.