The Conference South outfit came out of administration this week but have failed to meet the League's criteria despite sponsors Paddy Power agreeing to deposit a £100,000 bond with the membership committee.
The opening two fixtures against Chelmsford and Havant & Waterlooville have been postponed pending further discussions.
A Football Conference spokesman said "The new company do not satisfy our membership criteria".
"We cannot recognise Boro FC Ltd so the Newco is not a member of the Conference. We will now review this on Monday."