"flymake-same-files" produces wrong results when "flymake-run-in-place" is nil
I struggled with the problem for some time and figured out that when the following is used
(setq flymake-run-in-place nil)
the file, which is compared against the source file has temp suffix in the end, which causes "flymake-same-files" to return false when comparing e.g. these 2 files
"~/projects/some-path/models_flymake26065vXh.py"
"/home/user/projects/some-path/models.py"
This leads to wrong check results (no errors found, when they are present).
Hmm, interesting bug, thanks for the report.
As I understand the code, it should be trying to run flymake-same-files with the temp filename having been reverted to the original filename (in this case, the temp suffix being removed), that's done by flymake-get-real-file-name. If that's not doing its job then there'd be the symptoms you're describing.
I don't have time to take this further right now, but I'll try to find the time in the next few days.