We're in the process of installing a new Exchange 2003 server into a 5.5 environment.Originally when we began to do this we ran the Forestprep Check and Domainprep Check, however when we did this we ran into a problem where mailboxes were not linking to user accounts anymore.We didn't go any further when we ran into this issue, have been searching for help on it.But it seems to have fixed itself...Anyway, my question...Is there any reason Not to run the Forestprep and Domainprep Checks again?

Do issues at all, if they are the checks only. the domain prep can be run at anytime to reset permissions and such,just remember that the forest prep makes some schema changes that may effect things. Good luck and report back.

I'm assuming you mean your problem had nothing to do with the Schema extension and domain updates, but caused you to hold off on the Exchange 2003 deployment, which you are now ready to move forward with. You can attempt to manually re-run both /forestprep and /domainprep, but if they were previously successfully completed then the setup command will report that the updates have already been applied to your forest or domain.