My script under some conditions files into spam with addflag "\\Seen" and works as expected. Not sure why it wouldn't work for any folder since the addflag is done before the fileinto and knows nothing about the final disposition of the message when the addflag is done.
You said you reworked your sieve script. Maybe it has a bug. Have you tried it in Sieve Tester with a test case to see if its going down the expected path?
When I am not sure of where a case is going I debug it in sieve tester by sprinkling fileinto's in places I expect the test case to go. Since sieve tester doesn't care what you use for folder names I specifiy "point1", "point2", etc. as fileinto folder names just to see it goes down the expected path. The results of these fileinto's will display in the sieve tester results. The addflag's are reported in the results too (at least seen is).
Note, if you do copy your entire sieve script into sieve tester you must remove the "fcc" at the end of the require command since FM never updated sieve tester to support it. I submitted a ticket on this some time ago but FM just doesn't consider sieve tester a priority worth updating since they think so few users deal with sieve scripts.
I am not in a position to argue with that.