Okay, I have a client logo, white on black. Have converted the black to transparent and am trying to put a beveled edge on the white logo.
Problem is, the beveled portions take on horizontal lines which give the appearance of ridges in the lettering. I've seen this happen before with Photoshop-generated text, but altering the text point size makes the "ridges" go away. Have tried altering the image size of my client logo, but the "ridges" remain.
This uneven-ness or stair-stepping is probably related to your step of using the magic wand to delete the black background, the wand often produces jagged edges which are showing up more so when you apply the bevel - that's my guess at what's going on.
To solve it, hmmmm, starting from scratch with your original b/w logo as 1 layer, do a select all, and copy. Create a new layer and fill that layer with white. Add a layer mask to this layer (one of the button's at the bottom of the layer palette). Turn off your original layer. On the new white layer in the layer palette there'll be an extra rectangle representing your layer mask, ALT-click that to make it active - paste into it. ATL-click the same spot again to return to normal viewing. It should of pasted your original logo into the alpha of that layer - ie the layer mask - and should look like you'd expect your logo to. Try beveling that, it will hopefully be smoother.
OR if that seems confusing, from scratch you could just take your original layer, double click it to make sure it's not a background layer. Go into your layer style options ( same place your bevel is located) and on the 1st screen of options that appears at the bottom there's a section called "Blend if", use the sliders labelled "This Layer" and muck around with the black slider and use alt-drag to split the slider apart for a smooth transition, by twiddling with this and your bevel settings you should hopefully get something smoother too.
OR perhaps my guess on what's giving you issues is incorrect and none of these'll work. Make sure you have a high rez file.