With the Clip, at least with the OF, your computer only can see the files that were transferred in the USB mode that the computer then is connected to the Clip under. To avoid this issue, use one USB mode consistently, and avoid the Auto setting, which will start out trying to use MTP mode but then fall back to MSC mode, if necessary.
If you have transferred files in both MTP and MSC modes, to clean things up for you now, you could: transfer all your Clip's contents to your computer, doing it under both MTP and MSC modes; delete the content on the Clip; set the Clip to MSC mode; and transfer everything back. And then stay on MSC mode. (Note that if you update the OF, the Clip may reset to Auto mode--check it, and reset it to MSC.)