I just did a test:
my sheet:
A B
-- --
A =IF(A1<>"",A1,"")
B =IF(A2<>"",A2,"")
C =IF(A3<>"",A3,"")
D =IF(A4<>"",A4,"")
E =IF(A5<>"",A5,"")
F =IF(A6<>"",A6,"")
G =IF(A7<>"",A7,"")
H =IF(A8<>"",A8,"")
I =IF(A9<>"",A9,"")
J =IF(A10<>"",A10,"")
K =IF(A11<>"",A11,"")

=COUNTBLANK(B1:B11)

the countblank was "0", then I deleted "C"
and the countblank was 1
Deleted a few more, and it counted properly.
What do your formulas look like?
Can you send me the file directly?