Dual pedals often present problems like this, and it's not always easy to track it down.
Firstly, are you using battery or wall wart for your power? Sometimes you get hum or squeal when wall wart powered, but not when using a battery, so see if this is the case first.
If battery is ok, but you get squeal with a power supply, then the power supply is the cause of your noise.
Secondly, how is your cable management inside the enclosure? If your wiring is too long or messy, with power wires running alongside signal wires, this can induce squeal.
Try re-arranging your wires to keep power and signal wires as well seperated as possible.
If this helps, but does not cure the problem entirely, use grounded wire.
I use this stuff:
http://www.ebay.co.uk/itm/Van-Damme-Pro-Grade-Classic-XKE-1-Pair-Install-Cable-BY-THE-METRE-10-Colours-/181308920422?var=&hash=item2a36da9266I
always use grounded cable on
all my twin pedal builds - it makes a big difference!