Custom primer failed

[kal33na]

We had a customer submit a sample for sequencing which was prepared using a very unique library construction protocol that required a custom sequencing primer. I diluted the 100uM primer 1:200 in HT1, did a multi primer hyb on the cBOT. This sample failed with black tiles. qPCR using primers that match P5 and P7 sequences argued that his sample contained adapters and would be viable on the flowcell. He also said his sequencing primer worked in Sanger sequencing.

Any ideas on what could've gone wrong, or why a primer would work for Sanger and not for nextgen sequencing?

Thanks!

[IDDan]

Tm too low for HiSeq; sanger annealing is lower?