I'm not sure whether this will help, and I wouldn't yet call myself experienced either really, but how about the following?

• what does it mean that apache goes "temporarily down"? does it crash? lock up? does it come back up on its own, or do you have to restart it? when it is down, does it go stop responding completely, or does it just slow down or something similar?
• what do your logs say, especially your error log?
• what OS are you using?
• does it affect all sites you are hosting?
• does it affect all of the CGI programs?
• does it affect all of the CGI programs using DBI / DB_File::Lock?
• how long has this problem been persisting?
• have you made any software changes to the system?
• have you made any hardware changes to the system?
• can you observe any other malfunctioning on the system?
• did you check the scripts being used for races, potential deadlocks etc.?
• do you trust your users?

Also, can you use one of the hosted sites for debugging, or do they all have to be up for as much time as possible? And furthermore, have you tried DB_File::Lock 0.05?

I hope this helps a little bit at least.

--
mowgli