While not commonly used, you can specify glob patterns to most FTP servers via LIST, i.e. LIST -al *foo*. If you attempt to do this in FlashFXP and you have use MLSD checked it will convert that request into MLSD without any arguments and thus looses the glob pattern. You also can't manually enter any of the other list arguments ioFTPD accepts such as -R for recursive listings, etc because they all get lost. Remember, this is a manually typed list command. It probably shouldn't be automatically converted.....
On the other hand, if you attempt to type MLSD manually it fails because FlashFXP didn't detect it was a list command and open up a data connection like it does for LIST. It should definitely do that.
The MLSD standard says it accepts no commands, however on the servers I've been testing they usually do accept glob patterns. Therefore, a manually typed MLSD command should probably be passed in it's entirety and let the server ignore/reject unsupported formats.
Finally, you can specify a custom set of list arguments to pass to LIST commands but only as a general option and thus you can't customize it for particular sites. This features should probably be brought onto the site config menu where STAT, MLSD, etc are listed which probably needs to be turned into a radio box to pick one, and then a textfield for the custom args to pass...