Chimera.uchime high rate of false positives

Chimera.uchime has found over 60% of sequences in a dataset to be chimeric. Manual checking of a few hundred sequences has found no chimerae. Any ideas why this might be happening? Our chimera rate previously has been of the order of a few %. We get the same result using the sequences as their own reference and with Using mothur version 1.28.

Many thanks in advance for your help.

Could you send your input files to

also, how are you running chimera.uchime?