Testing the plugin provided in this Answer, I just saw that media_handle_sideload generates exactly this pattern, jpeg extension as well (instead of jpg).
Following its path through the core, it seems that only the filter wp_handle_upload could be used for dealing with that.
But a brief research shows an interesting use of wp_handle_upload_prefilter: Rename files during upload using variables.
A way of finding which element is using media_handle_sideload is:
– drop all the plugins and theme folders/files into a good editor (NotePad++, TextMate, etc) and do a global search for this filter.
After finding where it’s being called, a rename strategy can be thought of.
All this assuming the Sideload is responsible in OP’s case