The thing with using the Windows->Preferences etc. route, is that that just changes the settings for the current scheme. This is usefull for doing (for example) a single project in metric when you usually work with imperial measurements.
To change the default settings that each scene is created with, simply goto File->NewScene, when you change those settings, that's what you'll get everytime from then on.
As for the tool option, this is where the water can become a little muddy. The MEL command for the polygon cube on the polygons shelf is: "CreatePolygonCube". But, if you create your own shelf button for something, using ctrl-shift(select menu option you want a button for), the command is different! The MEL command for the polygon cube button on my _custom_ shelf reads "polyCube -w 1 -h 1 -d 1 -sx 1 -sy 1 -sz 1 -ax 0 1 0 -tx 1 -ch 1; objectMoveCommand;"
If I reset the tool settings and then change them to say x,y,z = 10, then hit create I get a 10x10x10 cube. If I move it away from the origin and then go to the polygons shelf and hit the cube button, it behaves as I would expect, and I get another 10x10x10 cube. If however I then go to my _custom_ shelf and hit the cube button, I get a 1x1x1 cube! So if the problem is with a custom button, just edit the MEL using the shelf-editor so that it is the same as the "original" button.
Something else worth mentioning, that you probably saw already is that above the menu option to "Reset Settings" for a tool, is the option "Save Settings".
As to reseting all tool settings at once - it's not something I'm aware of - perhaps could could nuke your prefs folder, but that'd kill any custom shelves you had, in addition to the custom defined units you already picked before, etc.
(Btw, thanx for that - I never realised the difference between the commands of default shelf buttons and custom ones before. That'll come in handy)