If "Move to location" is enabled for file conversion, the output file is deleted entirely if the output directory specified matches the temp directory specified under Options > File Naming.
To reproduce:
1) Go to Options > File Naming and Location Settings, and note the value of the Temporary File Location which is set there. (Copying to the clipboard would be a good idea.)
2) Right click an audio file > Library Tools > Convert format... > Options > Converter Settings > Move to location section > Enable (and set the location to the same temporary directory from above; paste it from the clipboard, whatever).
3) Click OK then click Start. The conversion will complete, and the output file will be... nowhere.
If you have an Explorer window open to the temp directory during the conversion, you can see the temporary output file created, then when the conversion process completes, it will be deleted. MC9 is "moving" the file, then unconditionally deleting it from the temp directory.
Here, I'll go the extra mile and help with the actual code:
if temp_dir = output_dir then
goto dont_delete_it_please
Just kidding (with the "code" above, not the problem report itself), I'll shutup now...