External air leaking into the chamber and residual moisture in the chamber etc. You can have your lyophilizer helium tested to find out leaks. First of all you should check whether the vacuum breaks due to permanent leaks or temperary leaks. If the pressure rise is constant over a period of time then it is the external air leaking in. If the pressure rise decays over a period of time then it is moisture inside the chamber. What leak rate you are observing? If you can't quantify it, give the dimensions of the chamber, initial pressure, final pressure and duration of pressure increase.
There is one good article in Pharmaceutical Engineering magazine(probably Jan or Feb issue)
It may not be unusual for your lyophilizer to leak.
Regards,