Research for this was a bit difficult. Engel only lists one of these variants and really doesn't go into any detail about it. I did some searches on Yahoo! Japan Auctions to see what I could find but that only really helped with one card. Luckily, however, I had been contacted by a Japanese card collector named Takashi last year who was interested in a trading cards. One of the cards that Takashi was looking were the Hideki Irabu cards I'll be mentioning in a moment. I asked him what the story was with those card and he told me. He also offered to answer any other questions I had about BBM cards and I took him up on the offer and asked about the other cards as well. While he didn't know about all the cards, he knew much more than I did about them so most of the following should be credited to him.
Here's the list:
1993 BBM #417 Takashi Wada
The original ('a') version of the card has a headshot of Goichi Inokubo on the back rather than Wada. I'm pretty sure what I have is the corrected ('b') version of the card:
I don't have a copy of the 'a' version but oddly enough, this is the card that Gary Engel uses as an example card for his listing of the 1993 set:
SCM #116 has the 'a' version of the card at 50 yen and the corrected version at 300 yen.
1993 BBM #477 Masanori Murakami
This is the variant that is listed by Engel. Takashi says "There is a notation error on the back side of the sentence" that was corrected on the 'b' version. I don't know which version I have but here's the back side of it:
SCM #116 has both versions of this card at 500 yen
1995 BBM #216 and #604 Hideki Irabu
These are kind of odd - technically the variation is with the gold signature parallel versions, not the base card. The 'a' version of the card is the base version. The 'b' version of the card has an incorrect gold signature on it - it's Ken Hirano instead of Irabu. The 'c' version of the card has the corrected signature. It's weird that the mistake was made on both the regular version of the card (#217) and the "Late Series" version (#604). I have the 'c' version of card #217 and the 'a' version of card #604.
SCM #116 has the 'a' and 'b' versions of card #216 at 400 yen while the 'c' version is 3000(!) yen. Version 'a' of #604 is listed at 500 yen while version 'b' is 1000 yen and version 'c' is 800 yen.
1999 BBM #464 Koichiro Yoshinaga
Takashi says that the original version of this card has an incorrect photo but he didn't know any more details about it. I don't have this card but I found this image on Yahoo! Japan Auctions. I don't know which version of the card this is although I'm pretty confident that this is Yoshinaga so it's probably the corrected version. SCM #116 has both versions listed at 50 yen.
1999 BBM 485 Naoyuki Ohmura
This is another case with an incorrect photo (kind of) but I think I understand what happened here. Notice in the above card that while the player's number on the card is 7, the player's uniform shows #60. Ohmura had worn #60 prior to 1999 when he switched his number to 7 so I think this is a picture of him with his old number (there's a possibility that this is a picture of Hironori Fujisaki who took uniform #60 in 1999 but it's unlikely as the little bit of the left sleeve patch looks like the one on the 1998 uniforms and Fujisaki was a pitcher). I don't have the corrected card but I found it on Yahoo! Japan Auctions (and the auction indicated that it was the corrected version):
SCM #116 has both versions of the card at 50 yen.
(And just so you know, Yoshinaga didn't change his number for 1999 so I don't think his card was corrected for that.)
2000 BBM #360 Seigo Fujishima
I've talked about this one before. This is the only one of these cards that I have both version of. The one on the left is the original and while the one on the right is the corrected version (obviously). Takashi did not know why the change was made although I think he thinks that the original photo is not Fujishima. SCM #116 has both cards at 50 yen.
2000 BBM #374 Takashi Yoshida and #377 Yuji Yoshioka
This is another issue with the head shots on the back of the cards - the head shots of the players are switched on the original ('a') version of the cards. So Yoshioka is on the back of Yoshida's card and Yoshida is on the back of Yoshioka's card:
Yoshioka's facial hair makes it kind of obvious. I don't have the corrected version of the cards and I couldn't find an image of them. SCM #116 has all four of the cards at 50 yen.
2001 BBM #284 Taka Miura
This is a fairly straight forward one - the original version of the card has the player's name as "Takashi Miura" rather than "Taka Miura". Here's the corrected version (from Yahoo! Japan Auctions):
SCM #116 has both versions of the card at....wait for it...50 yen yet again.
I don't know for sure but I'm pretty confident in saying that the corrected versions of the 1999-2001 cards were released as part of BBM's Late Series releases those years. I don't know how the corrected versions were released for 1993 and 1995 but the corrections may have been somewhat limited which would explain why some versions are more expensive than others.
SCM does not list the Reader/Leader variants from the 2000 BBM set as separate versions but obviously these are another example of corrected cards.
Thanks again to Takashi for all his help. Anything incorrect here is my fault, not his.