This sounds like a variation on the old "Nigerian"scam to me.
You pay the cheque into your account,it is (pending) cleared,which makes you assume you have the funds in your account.
The person/company who sent you the cheque writes/phone or emails to say the cheque had been sent in error,and can you repay them by cheque or bank transfer.
You being honest do so.
You then find that the cheque you paid in has been cancelled/recalled.
You loose the money,they gain it.
This may not be the case, as you say it is a reputable company,but it pays to be very wary these days!