5hmC levels could be very low and not even detectable with qPCR. Did you use the control DNA (5mC, 5hmC and unmodified)? If those gave the expected results, then did you run a qPCR of your fragment of interest without any restriction enzyme? Was the result positive (do you have enough DNA to start with)? NEB Epimark is based on the same technology / concept (beta-glycosylaytion of 5hmC) than Active Motif Specific Chemical Labelling (SCL) precipitation of 5hmC that can also be used for detection at a single locus, except that NEB doesn't use precipitation but 5hmC sensitive restriction enzymes. As a SCL user, I have also been confronted to very high Ct values (> 38) at some loci which are very poorly enriched in 5hmC. How many cycles of qPCR are you doing? I usually run at least 45 cycles. Good luck !