i've experienced the exact same thing. I hardly ever do rack lockouts nowadays, i think the 'sensation'your decribing is a result of your body genearating so much tension, (mainly for 2 reasons, your lifting above your max, and your moving the weight from the bottom postion) and then when you rest the bar onto the pins the load is suddenly removed,so your quickly going from max tension, to no tension, whether or not this is bad for i couldnt say, in my opinion, rack lockouts are great in moderation, my shoulders are fine, but i only do them every now and then, using a thick bar helps to restrict the weight, as does increasing the range of the lockout.
I read in one of Anthony dittilios articles to much bottom postion work can wear out the synovial surface of the joints, but i've never heard this any where else (not saying its never been said or written!) Also I'm sure i read that Dave Tate now favours the board press over the rack lockout as the rack lockout doesnt train the 'groove' and puts a lot of strain the shoulders.
Hope this helps...
