I've found workaround, installed dovecot-1.0.12, and now \Seen flags is storing. Rawlogs are attached. Recent versions of 1.0 and 1.1 branch are broken in this aspect, I have not tried branch 1.2 for this task.
--- bash-3.00# cat 20080725-140729-13208.in [skip] 4 UID fetch 1:* (FLAGS) 5 IDLE DONE 6 uid store 1:9,11 +Flags (\Seen) 7 IDLE DONE 8 close 9 logout bash-3.00# cat 20080725-140729-13208.out * OK [RAWLOG TIMESTAMP] 2008-07-25 14:07:29 * FLAGS (\Answered \Flagged \Deleted \Seen \Draft unknown-0) * OK [PERMANENTFLAGS ()] Read-only mailbox. * 11 EXISTS * 0 RECENT * OK [UNSEEN 1] First unseen. * OK [UIDVALIDITY 1216906855] UIDs valid * OK [UIDNEXT 12] Predicted next UID 3 OK [READ-ONLY] Select completed. * 1 FETCH (FLAGS () UID 1) * 2 FETCH (FLAGS () UID 2) * 3 FETCH (FLAGS (unknown-0) UID 3) * 4 FETCH (FLAGS () UID 4) * 5 FETCH (FLAGS () UID 5) * 6 FETCH (FLAGS () UID 6) * 7 FETCH (FLAGS () UID 7) * 8 FETCH (FLAGS () UID 8) * 9 FETCH (FLAGS () UID 9) * 10 FETCH (FLAGS (\Seen) UID 10) * 11 FETCH (FLAGS () UID 11) 4 OK Fetch completed. + idling 5 OK Idle completed. * 1 FETCH (UID 1 FLAGS (\Seen)) * 2 FETCH (UID 2 FLAGS (\Seen)) * 3 FETCH (UID 3 FLAGS (\Seen unknown-0)) * 4 FETCH (UID 4 FLAGS (\Seen)) * 5 FETCH (UID 5 FLAGS (\Seen)) * 6 FETCH (UID 6 FLAGS (\Seen)) * 7 FETCH (UID 7 FLAGS (\Seen)) * 8 FETCH (UID 8 FLAGS (\Seen)) * 9 FETCH (UID 9 FLAGS (\Seen)) * 11 FETCH (UID 11 FLAGS (\Seen)) 6 OK Store completed. + idling 7 OK Idle completed. 8 OK Close completed. * BYE Logging out 9 OK Logout completed. --- -- Sergey Ivanov.