Typically, a muzzle rear canted pancake would be worn closer to 4:00 than to 3:00.
The advantage of a leather pancake design is the retention provided by the outer layer of the holster closing up as it wraps around your body. Worn at 3:00, at the point of the hip, especially if you are thin, could cause problems since the holster could close up enough to make drawing and reholstering difficult. At 4:00, you probably have a flatter spot on your body that would allow the holster to function better.
With a kydex pancake, since they don't bend, 3:00 could cause problems since it isn't going to wrap around your hip and it may stick out a bit, or be somewhat painful as you found. On the good side, a kydex pancake won't have the same issues with reholstering or drawing that a leather holster will have, so you can probably wear it wherever you want as long as it is comfortable.
Edit to add: Lots of folks have had breakage with their hybrid IWB holsters when worn at 3:00 since the leather will flex and wrap around the hip, but the kydex won't, so the kydex will end up snapping at the attachment point with the leather backer.