What is in your commands.cfg file? (might be a differnt file on your system, i'm using ubuntu and nagios 3)
To troubleshoot I would go into my libexec-folder and try a "--help" on the script you are using.
Here is how I usually do it:
/usr/local/nagios/libexec# ./check_supa_script.pl -H 10.10.10.22 -r 10.10.10.4 -p 99,99 -t disks
In my case to remove "-p 99,99" would not give warnings and critical.