There seems to be some confusion about how shields work. Let me 'splain to y'all.
Each shield generator will create a specified number of shield points. Thus, a "100" point shield generator generates... 100 points of shields!
Shields take damage BEFORE non-shield skipping weapons do damage to either armor or components. The GENERATED SHIELD POINTS take the damage. Thus, a ship with 1 100 point generator will have 100 shield points. If hit with 2 40 kt damage shots, it will lose 80 points and only be worth 20. The next 40 point shot will kill the shield and "components" will take 20kt of damage.
Shields are not "randomly bypassed". Some weapons are listed as bypassing shields (eg, phased energy weapons). These do not reduce shields points, but rather ignore them causing damage to the ships components (unless, of course, it has armor).
There does seem to be a bug somewhere with some weapons vs shields where damage is "healed". I've sent Aaron a save file in which this happens reproducabley (sp?).
Hope that helps.
John