Flavie and/or ATMA bug report:
Flavie v1.4 (beta 11)
ATMA v5.05
Not sure if it can be easily reproduced, if it's been reported before, if it was Flavie or ATMA, or if it's even worth investigating, but here's what I was doing:
1. ATMA was open, however the file (runes.d2x) that I wanted the flavie report for was just closed. That stash file was changed within the active session of ATMA, so the ATMA generated .txt file should have been out of date (since I never update those files myself).
2. Open Flavie, change the output settings to whatever and list only the runes.d2x file as the source for the report.
3. Generate .txt and .html report files in Flavie, as normal.
... although the usual message appeared when generating the .txt files ("Generating ATMA text files for file <whateverpath>\runes.d2x" - or whatever the usual message is), from what I suspect the file wasn't generated properly. When I looked at the report, the rune quantities weren't updated from the last time I used Flavie (~3 months ago). Likewise, the runes tab in Flavie was also out of date.
To work around the problem:
1. In ATMA, open runes.d2x, make a minor addition/subtraction, and save the file again.
2. Close the ATMA application completely
3. Regenerate .txt and .html files in Flavie, as normal.
... after ATMA was fully closed the stash contents were reported properly from Flavie.