Im doing some northerns on my gene of interest. Im using the Dig-Riboprobe system. Whereby I clone my gene of interest into pGEM, linearise it in the direction of choice, and run off Dig-labeled RNA copies. I have performed the dig-labeling efficiency test and all my probes are to a greater or lesser degree labeled. As a positive control before testing on RNA samples I have performed a PCR on the original pGEM clones containing my gene of interest, run the band on a gel, denatured with NaOH and transferred to a blot. Then performed standard Northern protocols for the Dig system. 2 of 4 of my probes worked well, 2 did not work at all. Why not?

Probes are labeled, hybridization temp is 42, 52, 62, did not work on any of them. There clearly should not be a probe/target mismatch as they are the same thing. Any clues?