It takes hours before Mysql 4.1 is ready for connections

I am using Mysql 4.1 with windows 2K server.
After the service starts it takes 5 hours before the database is ready. Total size of DB files is 30 MB.
What is going wrong.> Anyone ideas about where I have to look.
I have liitle experience with Mysql

part of the logfile with shutdown and restart:
080527 0:38:14 InnoDB: Starting shutdown…
080527 0:38:16 InnoDB: Shutdown completed; log sequence number 0 885336
080527 0:38:16 [Note] C:\Program Files\MySQL\MySQL Server 4.1\bin\mysqld-nt: Shutdown complete

080527 5:42:45 InnoDB: Started; log sequence number 0 885336
C:\Program Files\MySQL\MySQL Server 4.1\bin\mysqld-nt: ready for connections.
Version: ‘4.1.14-nt’ socket: ‘’ port: 3306 Official MySQL binary

Hmm, From this part of log I see that it was stopped at 0:38, and then started at 5:42. Nothing happens in the middle… Can you please try stopping it manually, and then starting again (but not doing restart script, maybe it has some problem)?

A script stops the service, than backups the DB files, then restarts the service, I have seen that the service is running, but it takes that long before Mysql is accepting connections. (5 hours). When I restart manualy I get the same problem.