I was running Windower with Reshade 4.9.1 previously and saw the message about the new release 5.1 when logging in during the free login period.
After updating to 5.1, I found that if I tried to open a second Windower for a second character, the POL -> FFXI transition causes the Windower instance to crash without any pop up dialog box. The first Windower remains opened and I was able to control the character.
After trying a few times, I reverted back to 4.9.1 and was able to load the second (and third) Windower instance again.
Not sure whether it is a POL update or the Reshade change in 5.1 that cause the problem.