mIKE (sorry about that) a few thoughts.
a) is the affected shaft adjusted correctly, ie just a smidgen of end-float?
b) is there TOO much grease in the shaft? see suggestion g) i know its a bit of a long shot but…..
c) with the drive disconnected, can you feel any difference between the two shafts?
d) is the drive correctly adjusted, ie not too tight if belt driven, too much pressure on the affected shaft from one gear etc?
e) with all the grease wiped off, does the shaft slide in and out the tube cleanly, either shaft (ooohh matron), is the affected shaft bent?
f) can you run the boat with just one shaft connected at a time, dont know why, but I would try it just in case it reveals something.
g) does the affected shaft get warm/hot? try it in the bath until the shaft does something norty then you can feel it straight away.
h) is there water getting in?
i) are the drive belt/gears etc correctly lined up with the shaft? a ski-wiff drive would put pressure on a bearing, as g)
j) are your nuts tight? a loose nut might tighten after a while causing seizure
k) run out of ideas now…. anyone?? Ashley