Here's what I have found. I use two text editors simultaneously and usually this does not cause problems, but it seems to periodically in the find in files case.
I used my second text editor to global replace Log with AutoLog in a few .py files, then saved the changes, then switched to ST2 which had an open view onto one of the changed py files, and ST2 *did correctly show the AutoLog change (i.e. ST2 had detected the external edit and reloaded the py source). Then I did a search in files (ctrl+shift+F) for AutoLog in *.py and ST2 failed to find AutoLog. I repeated the find a couple of times and it failed each time. Then I made an unrelated edit using ST2 to one of the relevant py files and saved it, then repeated the find in files and only then did ST2 find AutoLog.
BTW in response to:
When ST2 says "0 matches across 0 files", "0 files" is not referring to the number of files that ST2 searched in, it refers to the number of files that contain matches. So this is going to be zero if no matches were found.