I had the same problem on Windows 10 with WAMP installed.
I shows on the phpinfo() but on the command prompt is gives the error.
When you enter c:\>php -m to show the available php modules its not there...
First look where your php.ini file is with the command:
c:\>php --ini
In my case: C:\wamp\bin\php\php5.6.19\php.ini
After editing this file and adding extension=php_phalcon.dll it works and when you enter then the phalcon command it gives you the available version and commands.
C:\>phalcon
C:\>phalcon-tools
Phalcon DevTools (3.0.1)
Available commands:
commands (alias of: list, enumerate)
controller (alias of: create-controller)
module (alias of: create-module)
model (alias of: create-model)
all-models (alias of: create-all-models)
project (alias of: create-project)
scaffold (alias of: create-scaffold)
migration (alias of: create-migration)
webtools (alias of: create-webtools)
How it helps someone.