You may want to check program priority. The conversions should be done at a lower priority so that they don't interfere with other programs.

You may also have a bottleneck with the hard drive. MediaMonkey will need to access both the media files and the database. If the hard drive is being maxed out it will cause not responding as MediaMonkey has to wait to get access to the database.

I am just getting to know MM so this is something I noticed, While converting many files to another format I use FreeAC as I can have 4 different encoding sessions running at one into different destination folders so as to avoid the pesky overwrite notification. If 2 or more are transcoding MM quits responding. This happens whithout fail prompting me to use VLC to listen to playback while running these jobs.
PS: Lovi'n MM so far.