That odd. I have 54/50 and it's reporting 3d13h for PM3. Maybe there's an inherent penalty in having higher brain cap even if you don't exceed it. I'll have to keep that in mind before buying any more Brain Cap cards.
I think the whole slowing down learning needs to be revisited entirely. Since TS discourages players making alts, eventually all players will learn all skills. I think the Brain Capacity upgrades should speed up learning, but I suggest the "over capacity" penalty be removed.