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May be it could sound you like an obvious response but anyway ... have you checked the max number of database served by filemaker server ?. Not sure about what was the default value in filemaker server 5.5 but it could be possible that you have reached the default limit with those new database that you are trying to serve.
Yes, increased the number to 80 from 50, then looked and saw we are currently serving 40. I also increased the mb allocation, just in case.
Thanks for the response, I'm sure I've done something wrong that's simple and possibly stupid!
One more thing, in the Events.log file it says "...could not be opened. Permission denied." I even tried this with a file stipped of any passwords and it did the same.
Check the OS level permissions on the databases, compared to the working database files.