Thanks Darren, for the list...these 11 cards correspond to this article explaining why these "variations" occurred.
http://www.oldbaseball.com/refs/1963_New_Variations.pdf
Here is list I found for the 63s variations that Richard Dingman complied ...most of these variances appear to be due to what was mentioned in the article above. My guess is the 341 Baldschun card, and the #29 & #54 Rookies cards would be the exceptions.
21 Keough Green extends to card edge White vertical line right of green box
Yellow vertical line right of green box
Blue vertical line right of green box
28 Fornieles Green extends to card edge White vertical line right of green box
Yellow vertical line right of green box
Blue vertical line right of green box
29 Rookie Stars 1962 1963
39 Angels G and E in "Angels" on back not connected G and E connected in "Angels" on back
40 Power Green extends to card edge White vertical line left of green box
Yellow vertical line left of green box
Blue vertical line left of green box
42 Williams Normal Blank back
52 Schilling White bat Red bat
54 Rookie Stars 1962 1963
79 Checklist 1 Has black border on top No black border on top
#79 shifted slightly right of center in box, names in bold
94 Schmidt Normal Blank back
102 Checklist 2 "Checklist" in white "Checklist" in red
105 Fairly Green extends to card edge White vertical line left of green box
Yellow vertical line left of green box - Have but yellow line is very thin
Blue vertical line left of green box
117 Davis Elbow does not touch red border in inset photo Elbow does touch red border in inset photo
121 Hannan Normal Stray orange line extending from copyright on back
134 Scheffing No green line on top of yellow box on front Partial green line on top of yellow box on front
143 WS Game 2 Yellow back Orange back
173 Bombers' Best No dark shadows around bat knob between Mick's legs Dark shadows around bat knob between Mick's legs
185 Hiller No black mark before "2 Yrs" in stat box Black mark before "2 Yrs" in stat box
191 Checklist 3 Box around 191 is square, yellow back Box around 191 is square, orange back
Box around 191 is rectangular, color bleed
224 Roarke Black mark under inset photo No black mark under inset photo
249 Burke Normal Leo Burke back, Jim Gentile front
274 Checklist 4 Large white box around 274, copyright symbol under "o" Small white box around 274, copyright symbol under "R"
341 Baldschun Polkadot slash across inset photo body White slash across inset photo body
362 Checklist 5 362 box is higher than wide 362 box is wider than high
Red and black boxes in front right margin, yellow bleeds into number box on back
372 Lee Normal Inset photo cropping variation
376 Wyatt Normal Inset photo cropping variation
382 Houk No ink blot Ink blot on left shoulder
386 Rookie Stars Normal Inset photo cropping variation
387 McBean Normal Inset photo cropping variation
388 Davenport Normal Inset photo cropping variation
404 Oldis Normal Inset photo cropping variation
409 Face Normal Inset photo cropping variation
413 Walker Stripe just shows on left shoulder Stripe does not show on left shoulder
431 Checklist 6 "Checklist" in black "Checklist" in white
438 Stock Normal Inset photo cropping variation
439 Zimmer Normal Inset photo cropping variation
445 Cash Normal Inset photo cropping variation
454 Fowler Card number not on white background Card number on white background
509 Checklist 7 Copyright to right Copyright centered
522 Rookie Stars Normal Orange stain under 1963 on front
527 Sadowski Normal Missing top border and parts of sides
Green line over yellow background
533 Shantz Normal Red stain covers face
567 Duffalo Normal White spot with black center on wrist in inset photo