You may get a runtime error with your 64 bit managed Windows Media Encoder application while the 32 bit application runs perfect.
This happens basically when your application tries to encode or more specifically transcode certain files that usually uses a 32 bit version of a third party CODEC. From the error it is impossible to guess the root cause but you can get a message saying “An unexpected error occurred with the video CODEC”.
To avoid such kind of errors a possible recommendation is to always use a 32 bit version of the WM Encoder application on 64 bit OS’s. That way you are also safe if you are using WM Encoder SDK for your application, since there is no 64 bit version of WM Encoder SDK.