As Ben said it's a matter of timing as I understand it. If the contract was issued for signing without objections from the contractor and he started work, not having objected then I believe that the courts would hold that a contract was in place.
If however the terms were objected to prior to the contract being issued for signing, or after the contract was issued but before work started, I believe the courts may look at the intent and hold that whilst the contract was in place the liquidated damages might not be enforceable.
If the contract was issued for signing after the work started and the contractor was unaware of the likely wording, you may have a problem with the contract as a whole.