I'd like to update this with how I managed to reproduce it. In the new example you're about to see, I had failed to reproduce it once already, so I had the pitcher Angel Guzman batting 7th and John Grabow warming up in the pen. When Guzman's spot came up, I pinch hit Xavier Nady for him. When the next half inning came up and I got the warning about having a position player on the mound, I selected John Grabow in the pen and chose "Double Switch." When the Double Switch menu came up, I chose "yes" to "Would you like to leave Xavier Nady in the game," and when it asked me to choose a position to move him to, I intentionally highlighted Xavier Nady's name on the list and pressed X. Then, I went up to Kosuke Fukudome's name and pressed X. Then, I went back to Xavier Nady's name and pressed X. After doing this, you return to gameplay with the aforementioned glitch in place. In this case, there are two Kosuke Fukudomes listed in the Batting Order, one at pitcher and one at RF. However, the pitcher is the real Kosuke Fukudome, while the right fielder is actually John Grabow.
One interesting thing I noticed is that the messed up John Grabow will have John Grabow's attributes in the field and when batting, but if you move him to the pitcher's spot, he will pitch using Fukudome's pitching attributes (because the system thinks he's Fukudome).
Here are some pictures I nabbed of it the other day:
Messed up Defensive Positioning screen:

Messed up Batting Order:

Fukudome on the mound:

Grabow (named Fukudome by the system) playing RF (taken at the same time as the above picture):

Here I swapped the two Fukudomes in the Defensive Positioning menu, which brought Grabow to the mound and put the real Fukudome in RF:

Here is Grabow (named Fukudome by the system) pitching during gameplay. Notice that he is limited to Fukudome's repertoire. In addition to this, he pitches just like Fukudome with 80 MPH fastballs, a changeup that barely breaks, and almost no control. If you look closely at the scoreboard, you can see the two Fukudomes listed on the batting order.

Here is the pitcher/batter display taken just after the above screenshot:

Here is Grabow coming up to bat. Notice something wrong with the graphic underneath him?



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