@charsbar @andk : If I go to "Delete Files" and select one checkbox for an upload which is not a normal perl distribution (e.g. a patch file), then all other non-distribution files are also selected. In the screenshot below I just clicked on one of the patch/* files:

The HTML for one entry looks like this:
<input data-distv="" name="pause99_delete_files_FILE" type="checkbox" value="patches/GD-2.56-RT114788-GREGOA.patch">
That is, data-distv is empty, which is probably causing the problem.
Maybe introduced by this change?
08e28db