My iPad was upgraded to iOS 7.0.6 a couple of weeks ago and the evasi0n jailbreak was applied soon after. I've always been using the var/mobile/media/downloads folder for storing various data downloaded from Safari and Atomic Web Browser, and I've never experienced any problems with this before.
However, a couple of days after the jailbreak was applied, all of the data (files and folders) stored in the downloads folder was gone without a trace. I was completely perplexed, as I've never experienced anything like that before. There was no sign of the data, not in the iFile trashcan or any other location. I wrote it off as a onetime fluke and continued to use the folder for storing downloaded data like before. Then yesterday the exact same thing happened again. All the data in the var/mobile/media/downloads folder is completely gone. I can't understand this, and to be honest I'm beginning to wonder if some sort of malware could be in play. Now, my iPad isn't loaded with apps or tweaks, not from Cydia or Appstore, so the list of suspects is limited.

Have any of you experienced anything like this? Is there a rational explanation for this besides malware, i.e. iFile or Atomic Web Browser somehow corrupting the data on exit or something like that?