The following should work.
q)(2;count x)#x,x
1 2 3
1 2 3
If you look at the parse tree of both your statements you can see that the second is evaluated differently. In the second only the result of count is passed as an argument to #.
q)parse"2 3#x,x"
#
2 3
(,;`x;`x)
q)parse"2 (count x)#x,x"
2
(#;(#:;`x);(,;`x;`x))