Unless you can give a reasonably sized code sample, it's difficult to tell. Anyway, the imperative F# version should be as efficient as the imperative C# version. I think one approach is to benchmark the two to see what is causing the difference (then someone can help with making that bit faster).
I briefly looked at your code and here are some assorted (untested) suggestions.
You can replace discriminated union Cell with an enum (this means you'll use value types and integer comparison instead of reference types and runtime type tests):
type Cell =
| Orange = 1
| Yellow = 2
| Barren = 3
You can mark some trivial functions as inline. For example:
let inline myincr (arr:int array) idx =
arr.[idx] <- arr.[idx] + 1
Don't use exceptions for control-flow. This is often done in OCaml, but .NET exceptions are slow and should be only used for exceptions. You can replace the for loop in your sample with a while loop and a mutable flag or with a tail-recursive function (a tail-recursive function is compiled into a loop, so it will be efficient, even in imperative solution).
