Hard to know for sure what the cause is with just the information in the question. Here are a couple of thoughts to help you find the cause of the problem:
1. Physico-chemical cause - are the particles strongly attracted to eachother / strongly repelled from the medium that contains them, in which case they will benefit from some kind of stabilizer in the matrix to help them be "happy".
2. Incomplete drying is often a cause of "cake" collapsse and aggregation in freeze drying. Look to understand the method and equipment you are using, to see if longer drying / different conditions are required. The depth of "cake" may also inhibit drying, and give you micro collapse in the middle of the vial / slab. Generally for nanomaterials a basic flask based freeze drying is going to cause you sadness, use one with refrigerated shelves so that you can get really good freezing, and control the drying nanomaterials.
General freeze drying hints and tips can be found here:
I'm afraid I can offer no help. Drying your particles will aggregate them as sure as night follows day... You cannot recover the original dispersed phase as you cannot recover drained marshes by adding water. The key is never to dry them...
In some cases (e.g. supported metal catalysts) then the nanoparticles can be kept stable and separate by means of the 'inert' support. See (registration required):
Rudy Rucker: 'I think dry nanotechnology is probably a dead-end' (August 2002)
Transhumanity magazine
Jim Adair: ‘If the particles are agglomerated and sub-micron it may be impossible to adequately disperse the particles……’
‘The energy barrier to redispersion is greater if the particles have been dried. Therefore the primary particles must remain dispersed in water….’
J H Adair, E. Suvaci, J Sindel, “Surface and Colloid Chemistry” Encyclopedia of materials: Science and Technology pp 8996 - 9006 Elsevier Science Ltd. 2001 ISBN 0-08-0431526