This throttling logic was added about a year ago when we noticed that Mac Mail was triggering IDS blocks when it tried to do NTLM authentication for POP, IMAP, and SMTP. For some reason, Mac Mail would attempt NTLM authentication multiple times in short period without indicating to the user that something was wrong or trying a different authentication method. The log snippet you provided actually shows similar behavior. The first two lines are the first attempt, which does get counted toward the IDS rules. The third and fourth lines indicate a second authentication attempt that isn't being counted due to the throttling.
As for disabling NTLM, that isn't currently possible in SmarterMail. Further, SmarterMail natively processes NTLM authentication without relying on Windows, which is why the registry and group policy settings have no impact on SmarterMail's behavior.
Andrew Barker
Lead Software Developer
SmarterTools Inc.
www.smartertools.com