There are several attributes to the Find function. The majority of these are automatically set by Excel based on the most recent use. Excel will remember your most recent option even if you last used Find manually. Therefore, while using VBA, all pertinent properties should be set.
Dim foundRng As Range
Set foundRng = Range("F1:F2000").Find(What:="9999", _
After:=Cells(2000, "F"), _
If foundRng Is Nothing Then
MsgBox "Value not found"
The LookIn property, which I believe your system currently uses xlFormulas (it's xlValuesabove), is the most likely cause of your issue. The formula and value of a cell are the same when it contains a hard value, such as 9999. However, if the formula is =3*3333, the value and the formula diverge, and the number 9999 is not found in the formula.