Lotus Domino Consistency Checker running upon reboot....

Consistency runs whenever Domino terminates abnormally with Notes databases in use.  To terminate properly, you need to use the Quit command in the Domino Console or stop the Windows Service.  Reboot, power cycle, etc. won't shut down Domino properly.  
Or is your question more along:  I cannot control abnormal termination of Domino (other factors in the server) I want to postpone consistency check for specific databases?
Note that Domino will not start without a consistency check of log.nsf, mail.box, names.nsf and other system databases.

Hi, thanks. We are shutting it down correctly and was wanting to avoid the long consistency check when it is restarted. I think you answered my question that it runs it anyways on all the system databases and we can't avoid that. So is there a way to exclude the users mailbox databases from the consistency check or are they considered system databases as well? I would assume that if I could exclude the users mailboxes from the consistency check I would more than likely save a lot of time. Is that a possibility without moving heaven and earth?

Check also what the size if of log.nsf and mail.box. Do you ever check what's in mail.box? The Admin is supposed to clean up that database regularly, for all dead mail can become a real burden for the system.

Hi there,,

In addition to the suggetions of the other experts I have some things to talk about ..

- Could you please give me a hint about the other resources of the server ? ...
    - Is it a Physical or a Virtual one ?
    - What is the operating system of the server  ?
    - What are the details of the HDDs, Memory , CPU etc.

Actually, I used to have this problem with some of my servers and still I have it with some other ones , It takes more than 2 hours because I have a lot of large lotus databases and the consistency process take some time on each one of them .So, I highy recommend you first to make sure that the databases of the users are not growing in an aggressive way.

Finally, this issue was solved with one of my servers just after we replace the Hardware with a more powerful one and the OS with Win2k8 R2 so it takes now 15 minutes only .

Best Wishes

@akhafaf: my answer applies to you too.  It is NOT normal to start Domino and experience delays due to consistency checking.  This is the same as driving on with an engine warning light on in your car.  Continuing to do this is choosing to live life dangerously and taking unwaranted risks with your data.