Have you apply the Template hotfix for BBProfiles.ntf file?
Service Pack Download:-
https://www.blackberry.com/Downloads/
Not sure if it is related... For its release notes:
SDR 86377
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In BlackBerry Enterprise Server Version 4.0 SP4 and later, an incorrect template file might have delayed the BlackBerry Enterprise Server startup process.
You must update the BBProfiles.ntf file.
1.Obtain the updated BBProfiles.ntf file from Research In Motion.
2.If your IBMxxx174; Lotusxxx174; Dominoxxx174; server is set to start automatically, turn off this setting.
3.In the Domino Server Console, type quit.
4.In <drive>\Lotus\Domino\Data, replace the existing BBProfiles.ntf file with the updated version.
5.Start the Domino Server Console.
But in any case, always upgrade to the latest service pack + hotfix... now the latest is SP4 hotfix 3....